Early goal enteral nutrition associated with decreased in-hospital death in mechanically ventilated critically ill adults: a retrospective cohort study

INTRODUCTION

Early enteral nutrition (EN) in critically ill adult patients is thought to improve mortality and morbidity; expert guidelines recommend early initiation of EN in critically ill adults. However, the ideal schedule and dose of EN remain understudied.

STUDY OBJECTIVE

Our objective was to evaluate the relationship between achieving 70% of recommended EN within 2 days of intubation ('early goal EN') and clinical outcomes in mechanically ventilated medically critically ill adults. We hypothesised that early goal EN would be associated with reduced in-hospital death.

METHODS

We conducted a retrospective cohort study of mechanically ventilated adult patients admitted to our medical intensive care unit during 2013-2019. We assessed the proportion of recommended total EN provided to the patient each day following intubation until extubation, death or 7 days whichever was shortest. Patients who received 70% or more of their recommended total daily EN within 2 days of intubation (ie, 'baseline period') were considered to have achieved 'early goal EN'; these patients were compared with patients who did not ('low EN'). The primary outcome was in-hospital death; secondary outcomes were successful extubation and discharge alive.

RESULTS

938 patients met eligibility criteria and survived the baseline period. During the 7-day postintubation period, 64% of all patients reached 70% of recommended daily calories; 33% of patients achieved early goal EN. In unadjusted and adjusted models, early goal EN versus low EN was associated with a lower incidence of in-hospital death (subdistribution HR (SHR) unadjusted=0.63, p=0.0003, SHR adjusted=0.73, p=0.02). Early goal EN was also associated with a higher incidence of successful extubation (SHR unadjusted=1.41, p<0.00001, SHR adjusted=1.27, p=0.002) and discharge alive (SHR unadjusted=1.54, p<0.00001, SHR adjusted=1.24, p=0.02).

CONCLUSIONS

Early goal EN was associated with significant improvement in clinical metrics of decreased in-hospital death, increased extubation and increased hospital discharge alive.

Intensive care unit interventions to promote sleep and circadian biology in reducing incident delirium: a scoping review

RATIONALE/OBJECTIVES

Despite plausible pathophysiological mechanisms, research is needed to confirm the relationship between sleep, circadian rhythm and delirium in patients admitted to the intensive care unit (ICU). The objective of this review is to summarise existing studies promoting, in whole or in part, the normalisation of sleep and circadian biology and their impact on the incidence, prevalence, duration and/or severity of delirium in ICU.

METHODS

A sensitive search of electronic databases and conference proceedings was completed in March 2023. Inclusion criteria were English-language studies of any design that evaluated in-ICU non-pharmacological, pharmacological or mixed intervention strategies for promoting sleep or circadian biology and their association with delirium, as assessed at least daily. Data were extracted and independently verified.

RESULTS

Of 7886 citations, we included 50 articles. Commonly evaluated interventions include care bundles (n=20), regulation or administration of light therapy (n=5), eye masks and/or earplugs (n=5), one nursing care-focused intervention and pharmacological intervention (eg, melatonin and ramelteon; n=19). The association between these interventions and incident delirium or severity of delirium was mixed. As multiple interventions were incorporated in included studies of care bundles and given that there was variable reporting of compliance with individual elements, identifying which components might have an impact on delirium is challenging.

CONCLUSIONS

This scoping review summarises the existing literature as it relates to ICU sleep and circadian disruption (SCD) and delirium in ICU. Further studies are needed to better understand the role of ICU SCD promotion interventions in delirium mitigation.

Morning Chronotype Is Associated with Improved Adherence to Continuous Positive Airway Pressure among Individuals with Obstructive Sleep Apnea

Rationale: Poor adherence limits the effectiveness of continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea (OSA). A better understanding of CPAP adherence is needed to develop novel strategies to improve it. Objectives: To determine if the chronotype (morning, evening, or intermediate) of patients with OSA is associated with differences in CPAP adherence. If such an association exists, determine the mechanisms underlying this association. Methods: We performed a secondary analysis of the APPLES (Apnea Positive Pressure Long-term Efficacy Study) clinical trial. We assessed chronotype using the Morningness-Eveningness Questionnaire (MEQ) among participants randomized to the CPAP arm with daily adherence data (n = 469). Evening (MEQ ⩽ 41), intermediate (41 < MEQ < 59), and morning type (MEQ ⩾ 59) categories were the exposures. We modeled daily CPAP use (hours per night) over a 6-month period, using a linear mixed model, adjusted for covariates (e.g., age, sex, marital status). To assess mechanisms of the association, we performed mediation analyses using sleep duration, weekend catch-up sleep, depression, and other factors. Results: Most participants were obese men with severe OSA (body mass index of 32.3 ± 7.3 kg/m2, 65% male, and apnea-hypopnea index 39.8 ± 24.6/h). Participants were 44% morning, 47% intermediate, and 8% evening chronotype. Participants with the morning chronotype reported the shortest sleep duration on weekends (7.3 vs. 7.6 and 7.9 h/night) compared with the intermediate and evening types. Participants with the morning chronotype exhibited a 40-min/night higher CPAP use (P = 0.001) than persons with the intermediate chronotype. This relationship was mildly attenuated (32.8 min/night; P = 0.011) after adjustment for covariates. None of the selected factors (e.g., sleep duration, weekend catch-up sleep) exhibited a significant mediation effect. Conclusions: Morning chronotype is associated with a clinically meaningful increase in CPAP adherence compared with other chronotypes. Mechanisms of this association require further study. Chronotype may be a novel predictor of CPAP adherence. Clinical trial registered with www.clinicaltrials.gov (NCT00051363).

Causes, Consequences, and Treatments of Sleep and Circadian Disruption in the ICU: An Official American Thoracic Society Research Statement

Background: Sleep and circadian disruption (SCD) is common and severe in the ICU. On the basis of rigorous evidence in non-ICU populations and emerging evidence in ICU populations, SCD is likely to have a profound negative impact on patient outcomes. Thus, it is urgent that we establish research priorities to advance understanding of ICU SCD. Methods: We convened a multidisciplinary group with relevant expertise to participate in an American Thoracic Society Workshop. Workshop objectives included identifying ICU SCD subtopics of interest, key knowledge gaps, and research priorities. Members attended remote sessions from March to November 2021. Recorded presentations were prepared and viewed by members before Workshop sessions. Workshop discussion focused on key gaps and related research priorities. The priorities listed herein were selected on the basis of rank as established by a series of anonymous surveys. Results: We identified the following research priorities: establish an ICU SCD definition, further develop rigorous and feasible ICU SCD measures, test associations between ICU SCD domains and outcomes, promote the inclusion of mechanistic and patient-centered outcomes within large clinical studies, leverage implementation science strategies to maximize intervention fidelity and sustainability, and collaborate among investigators to harmonize methods and promote multisite investigation. Conclusions: ICU SCD is a complex and compelling potential target for improving ICU outcomes. Given the influence on all other research priorities, further development of rigorous, feasible ICU SCD measurement is a key next step in advancing the field.

Keeping an eye on circadian time in clinical research and medicine

BACKGROUND

Daily rhythms are observed in humans and almost all other organisms. Most of these observed rhythms reflect both underlying endogenous circadian rhythms and evoked responses from behaviours such as sleep/wake, eating/fasting, rest/activity, posture changes and exercise. For many research and clinical purposes, it is important to understand the contribution of the endogenous circadian component to these observed rhythms.

CONTENT

The goal of this manuscript is to provide guidance on best practices in measuring metrics of endogenous circadian rhythms in humans and promote the inclusion of circadian rhythms assessments in studies of health and disease. Circadian rhythms affect all aspects of physiology. By specifying minimal experimental conditions for studies, we aim to improve the quality, reliability and interpretability of research into circadian and daily (i.e., time-of-day) rhythms and facilitate the interpretation of clinical and translational findings within the context of human circadian rhythms. We describe protocols, variables and analyses commonly used for studying human daily rhythms, including how to assess the relative contributions of the endogenous circadian system and other daily patterns in behaviours or the environment. We conclude with recommendations for protocols, variables, analyses, definitions and examples of circadian terminology.

CONCLUSION

Although circadian rhythms and daily effects on health outcomes can be challenging to distinguish in practice, this distinction may be important in many clinical settings. Identifying and targeting the appropriate underlying (patho)physiology is a medical goal. This review provides methods for identifying circadian effects to aid in the interpretation of published work and the inclusion of circadian factors in clinical research and practice.

A SAS macro for modelling periodic data using cosinor analysis

BACKGROUND AND OBJECTIVE

Cosinor analysis, developed by Franz Hallberg and colleagues in the 1960s, allows for the fitting of a cosine curve to data of a known period. Cosinor analysis is frequently used in the analysis of biological rhythm data. While software exists to perform these analyses, we are not aware of any published SAS procedures or macros which would facilitate them.

METHODS

To meet this gap, we herein describe SAS macros which perform cosinor analyses that assume either normally or gamma distributed outcomes and fixed period. The macros can 1) produce datasets with cosinor parameters including acrophase, mesor, amplitude, nadir and test for rhythmicity 2) output datasets with fitted and observed values from the model, and 3) plot the resulting curve and underlying data.

RESULTS

We demonstrate the use of these macros with data from our research on circadian rhythms of heart rate and sleep in critically ill patients.

CONCLUSIONS

Cosinor analysis provides a parsimonious and intuitive set of estimates to summarize periodic data. We are hopeful that the publication of our macro will allow a wider spectrum of users to avail themselves of this technique.

Light Levels in ICU Patient Rooms: Dimming of Daytime Light in Occupied Rooms

One-third of patients report disruption of sleep by overnight light. Importantly, light causes both immediate sleep disturbance and influences circadian function, a fundamental process underpinning high-quality sleep. Short bursts of light at night and/or lack of bright daytime light disrupt circadian alignment, leading to sleep deficiency. To improve understanding of 24-hour light patterns, we conducted a longitudinal study of light levels in intensive care unit (ICU) rooms. Over 450 room-days, we observed high variability, dim daytime light, and active dimming of natural sunlight in occupied rooms. Such noncircadian light patterns have multifactorial influences on sleep and are a key target for sleep improvement in the ICU.

A Clinic Blueprint for Post-Coronavirus Disease 2019 RECOVERY: Learning From the Past, Looking to the Future

The severe acute respiratory syndrome coronavirus 2 pandemic poses extraordinary challenges. The tremendous number of coronavirus disease 2019 (COVID-19) cases in the United States has resulted in a large population of survivors with prolonged postinfection symptoms. The creation of multidisciplinary post-COVID-19 clinics to address both persistent symptoms and potential long-term complications requires an understanding of the acute disease and the emerging data regarding COVID-19 outcomes. Experience with severe acute respiratory syndrome and Middle East respiratory syndrome, post-acute respiratory distress syndrome complications, and post-intensive care syndrome also informs anticipated sequelae and clinical program design. Post-COVID-19 clinical programs should be prepared to care for individuals previously hospitalized with COVID-19 (including those who required critical care support), nonhospitalized individuals with persistent respiratory symptoms following COVID-19, and individuals with preexisting lung disease complicated by COVID-19. Effective multidisciplinary collaboration models leverage lessons learned during the early phases of the pandemic to overcome the unique logistical challenges posed by pandemic circumstances. Collaboration between physicians and researchers across disciplines will provide insight into survivorship that may shape the treatment of both acute disease and chronic complications. In this review, we discuss the aims, general principles, elements of design, and challenges of a successful multidisciplinary model to address the needs of COVID-19 survivors.

Pilot Observational Study to Detect Diurnal Variation and Misalignment in Heart Rate Among Critically Ill Patients

Circadian disruption is common in critically ill patients admitted to the intensive care unit (ICU). Understanding and treating circadian disruption in critical illness has significant potential to improve critical illness outcomes through improved cognitive, immune, cardiovascular, and metabolic function. Measurement of circadian alignment (i.e., circadian phase) can be resource-intensive as it requires frequent blood or urine sampling over 24 or more hours. Less cumbersome methods of assessing circadian alignment would advance investigations in this field. Thus, the objective of this study is to examine the feasibility of using continuous telemetry to assess diurnal variation in heart rate (HR) among medical ICU patients as a proxy for circadian alignment. In exploratory analyses, we tested for associations between misalignment of diurnal variation in HR and death during hospital admission. This was a prospective observational cohort study embedded within a prospective medical ICU biorepository. HR data were continuously collected (every 5 s) via telemetry systems for the duration of the medical ICU admission; the first 24 h of this data was analyzed. Patients were extensively characterized via medical record chart abstraction and patient interviews. Of the 56 patients with complete HR data, 48 (86%) had a detectable diurnal variation. Of these patients with diurnal variation, 39 (81%) were characterized as having the nadir of their HR outside of the normal range of 02:00–06:00 (“misalignment”). Interestingly, no deaths occurred in the patients with normally aligned diurnal variation; in contrast, there were seven deaths (out of 39 patients) in patients who had misaligned diurnal variation in HR. In an exploratory analysis, we found that the odds ratio of death for misaligned vs. aligned patients was increased at 4.38; however, this difference was not statistically significant (95% confidence interval 0.20–97.63). We conclude that diurnal variation in HR can be detected via continuous telemetric monitoring of critically ill patients. A majority of these patients with diurnal variation exhibited misalignment in their first 24 h of medical ICU admission. Exploratory analyses suggest possible associations between misalignment and death.

Circadian Biology and Its Importance to Intensive Care Unit Care and Outcomes

Circadian rhythms are an integral part of life on earth. Circadian rhythms play a fundamental role in homeostasis as they ensure coordination between the environment and an organism's behavior and physiology. This coordination is called entrainment. Entrainment depends on environmental cues known as zeitgebers. Human zeitgebers include light (primary zeitgeber), sleep, eating, exercise, and activity. Circadian rhythms are disrupted in critically-ill patients due to both critical illness and current intensive care unit (ICU) practices. Disruptions in circadian rhythms are tightly linked with ICU sleep disruption. Together these entities potentiate numerous adverse outcomes including delirium, metabolic derangements, cardiovascular instability, and immune compromise. Herein, we will highlight potential areas for care improvement via chronobundles. We suggest bright light during the day, maintaining darkness, and protecting sleep at night, intermittent rather than continuous feeds, and activity via mobilization during the day. Optimizing circadian rhythms is a low-risk intervention that is underutilized in current ICU practice. This optimization could be a powerful tool in helping to improve outcomes in the critically-ill patient.

Pilot study: an intensive care unit sleep promotion protocol

Purpose

Disturbances, such as in-room activity and sound, are significant sources of sleep disruption among critically ill patients. These factors are potentially modifiable. We tested the impact of an intensive care unit (ICU) sleep promotion protocol on overnight in-room disturbance.

Methods

Our protocol restricted non-urgent bedside care from 00:00 to 03:59. Patients were assigned to usual care (n=30) or the sleep protocol (n=26). The primary outcomes were measures of in-room activity, sound and light. These three types of disturbance were compared between arms during a baseline time block (20:00–23:59) and a rest time block (00:00–03:59). We assessed the sleep protocol effect with generalised linear models.

Results

Usual care and sleep protocol patients had equivalent levels of in-room activity, sound and light during the baseline time block (20:00–23:59). In contrast, during the rest time block (00:00–03:59), the sleep protocol arm had 32% fewer room entries (rate ratio (RR) 0.68, p=0.001) and 9.1 fewer minutes of in-room activity (p=0.0002). Also, the length of time between room entrances increased from 26.4 to 45.8 min (p=0.0004). The sleep protocol arm also had lower sound during the rest time block. Mean A-weighted sound was 2.5 decibels lower (p=0.02), and there were 36% fewer peaks (RR 0.64, p=0.02). Light levels were highly variable and not changed by the sleep protocol.

Conclusions

Sleep promotion protocols can improve in-room activity and sound. This provides a better sleep opportunity and may, therefore, improve ICU sleep.

Trial registration number

1112009428

Association between death and loss of stage N2 sleep features among critically Ill patients with delirium

PURPOSE

Critically ill patients experience significant sleep disruption. In this study of ICU patients with delirium, we evaluated associations between the loss of stage N2 features (K-complexes, sleep spindles), grade of encephalopathy based on electroencephalography (EEG), and intensive care unit (ICU) outcomes. We hypothesized that loss of stage N2 features is associated with more severe grades of encephalopathy and worse ICU outcomes including death.

MATERIALS AND METHODS

This was an observational cohort study of 93 medical ICU patients without primary acute brain injury who underwent continuous EEG. Type and severity of critical illness, sedative-hypnotic use, length of stay, modified Rankin Scale at hospital discharge, and death during hospitalization were abstracted from the medical record. EEG was evaluated for grade of encephalopathy and sleep features.

RESULTS

Patients without K-complexes or without sleep spindles had more severe encephalopathy and higher odds of death. The odds ratio for patients without K-complexes was 18.8 (p = .046). The odds ratio for patients without sleep spindles was 6.3 (p = .036).

CONCLUSIONS

Loss of stage N2 features is common and associated with more severe encephalopathy and higher odds of death. The absence of either Stage N2 feature, K complexes or sleep spindles, may have important prognostic value.

Non-circadian signals in the intensive care unit: Point prevalence morning, noon and night

BACKGROUND

Intensive care unit (ICU) sleep disturbance is severe and potentially related to abnormal light and sound exposure.

OBJECTIVES

To assess the prevalence of measures of light and sound disturbance in ICU patient rooms, and whether these could be modified by a sleep-promotion intervention.

METHODS

This observational study with a before and after design for a quality improvement initiative surveyed environmental factors in ICU rooms at 01:00 08:00, and 12:00. Surveys assessed light usage, television usage, window shade position, and room door/curtain position. Factors were compared before and after an ICU sleep-promotion intervention.

RESULTS

990 (pre-intervention) and 819 (post-intervention) occupied rooms were surveyed. Pre-intervention, the prevalence of night-time factors included: bright lights on (21%), television on (46%), and room door open (94%). Post-intervention, more rooms had all lights off at night (41% v 50%, p = 0.04), and fewer rooms had open door curtains (57% v 42%, p = 0.001) and window shades (78% v 62%, p = 0.002).

CONCLUSIONS

Disruptive environmental factors are common in the ICU. Some factors improve with sleep-promotion interventions.

Association of intensive care unit delirium with sleep disturbance and functional disability after critical illness: an observational cohort study

Background

In medical intensive care unit (MICU) patients, the predictors of post-discharge sleep disturbance and functional disability are poorly understood. ICU delirium is a risk factor with a plausible link to sleep disturbance and disability. This study evaluated the prevalence of self-reported post-ICU sleep disturbance and increased functional disability, and their association with MICU delirium and other ICU factors.

Methods

This was an observational cohort study of MICU patients enrolled in a biorepository and assessed upon MICU admission by demographics, comorbidities, and baseline characteristics. Delirium was assessed daily using the Confusion Assessment Method for the ICU. Telephone follow-up interview instruments occurred after hospital discharge and included the Pittsburgh Sleep Quality Index (PSQI), and basic and instrumental activities of daily living (BADLs, IADLs) for disability. We define sleep disturbance as a PSQI score > 5 and increased disability as an increase in composite BADL/IADL score at follow-up relative to baseline. Multivariable regression modeled the associations of delirium and other MICU factors on follow-up PSQI scores and change in disability scores.

Results

PSQI and BADL/IADL instruments were completed by 112 and 122 participants, respectively, at mean 147 days after hospital discharge. Of those surveyed, 63% had sleep disturbance by PSQI criteria, and 37% had increased disability by BADL/IADL scores compared to their pre-MICU baseline. Total days of MICU delirium (p = 0.013), younger age (p = 0.013), and preexisting depression (p = 0.025) were significantly associated with higher PSQI scores at follow-up. Lower baseline disability (p < 0.001), older age (p = 0.048), and less time to follow-up (p = 0.024) were significantly associated with worsening post-ICU disability, while the occurrence of MICU delirium showed a trend toward association (p = 0.077).

Conclusions

After adjusting for important covariates, total days of MICU delirium were significantly associated with increased post-discharge sleep disturbance. Delirium incidence showed a trend toward association with increased functional disability in the year following discharge.

Creating Naptime: An Overnight, Nonpharmacologic Intensive Care Unit Sleep Promotion Protocol

Introduction:

Patients in the intensive care unit (ICU) have significantly disrupted sleep. Sleep disruption is believed to contribute to ICU delirium, and ICU delirium is associated with increased mortality. Experts recommend sleep promotion as a means of preventing or shortening the duration of delirium. ICU Sleep promotion protocols are highly complex and difficult to implement. Our objective is to describe the development, pilot implementation, and revision of a medical ICU sleep promotion protocol.

Methods:

Naptime is a clustered-care intervention that provides a rest period between 00:00 and 04:00. We used literature review, medical chart review, and stakeholder interviews to identify sources of overnight patient disturbance. With stakeholder input, we developed an initial protocol that we piloted on a small scale. Then, using protocol monitoring and stakeholder feedback, we revised Naptime and adapted it for unitwide implementation.

Results:

We identified sound, patient care, and patient anxiety as important sources of overnight disturbance. The pilot protocol altered the timing of routine care with a focus on medications and laboratory draws. During the pilot, there were frequent protocol violations for laboratory draws and for urgent care. Stakeholder feedback supported revision of the protocol with a focus on providing 60- to 120-minute rest periods interrupted by brief clusters of care between 00:00 and 04:00.

Discussion:

Four-hour blocks of rest may not be possible for all medical ICU patients, but interruptions can be minimized to a significant degree. Involvement of all stakeholders and frequent protocol reevaluation are needed for successful adoption of an overnight rest period.

Factors Influencing Patients' Sleep in the Intensive Care Unit: Perceptions of Patients and Clinical Staff

BACKGROUND

Multiple factors are believed to contribute to disruption of patients' sleep and negatively affect clinical outcomes in the intensive care unit. Achieving restorative sleep for critically ill patients remains a challenge.

OBJECTIVES

To explore the perceptions and beliefs of staff, patients, and surrogates regarding the environmental and nonenvironmental factors in the medical intensive care unit that affect patients' sleep.

METHODS

This qualitative study included 24 medical intensive care unit staff (7 physicians, 5 respiratory therapists, 10 nurses, and 2 patient-care assistants), 8 patients, and 6 patient surrogates. Semistructured interviews were conducted, and qualitative analysis of content was used to code, categorize, and identify interview themes.

RESULTS

Interview responses revealed 4 themes with related subthemes: (1) The overnight medical intensive care unit environment does affect sleep, (2) nonenvironmental factors such as difficult emotions and anxiety also affect sleep, (3) respondents' perceptions about sleep quality in the medical intensive care unit were highly variable, and (4) suggestions for sleep improvement included reassuring patients and care-clustering strategies.

CONCLUSIONS

Results of this study suggest that environment is not the only factor influencing patients' sleep. Decreases in environmental sources of disturbance are necessary but not sufficient for sleep improvement. Guideline-recommended clustered care is needed to provide adequate sleep opportunity, but patients' emotions and anxiety also must be addressed.

Sleep and sleep disordered breathing in hospitalized patients

Sleep is a fundamental physiological process necessary for recovery from acute illness. Unfortunately for hospitalized patients, sleep is often short, fragmented, and poor in quality, and may be associated with adverse outcomes including inpatient delirium. Many factors contribute to poor sleep in the hospital setting, including preexisting sleep deprivation, sleep disordered breathing, environmental noise and light, patient care activities, and medications. Sleep disordered breathing increases the risk of potentially life-threatening cardiovascular, respiratory, and metabolic consequences, and therefore should be diagnosed and treated in hospitalized patients. Mitigating the sequelae associated with poor sleep quality and sleep disordered breathing requires early identification of modifiable factors impacting a patient's sleep, including engagement of a multidisciplinary team. In this article, we review the current knowledge of sleep in hospitalized patients with a detailed focus on patients with sleep disordered breathing.

Feasibility study of unattended polysomnography in medical intensive care unit patients

OBJECTIVES

To evaluate the feasibility of using unattended, portable polysomnography (PSG) to measure sleep among patients in the medical intensive care unit (MICU).

BACKGROUND

Accurate measurement of sleep is critical to studies of MICU sleep deprivation. Although PSG is the gold standard, there is limited data regarding the feasibility of utilizing unattended, portable PSG modalities in the MICU.

METHODS

MICU based observational pilot study. We conducted unattended, 24-h PSG studies in 29 patients. Indicators of feasibility included attainment of electroencephalography data sufficient to determine sleep stage, sleep efficiency, and arousal indices.

RESULTS

Electroencephalography data were not affected by electrical interference and were of interpretable quality in 27/29 (93%) of patients. Overnight sleep efficiency was 48% reflecting a mean overnight sleep duration of 3.7 h.

CONCLUSIONS

Unattended, portable PSG produces high quality sleep data in the MICU and can facilitate investigation of sleep deprivation among critically ill patients. Patient sleep was short and highly fragmented.

Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids

β-Thalassemia is a genetic disorder caused by mutations in the β-globin gene. Triplex-forming oligonucleotides and triplex-forming peptide nucleic acids (PNAs) have been shown to stimulate recombination in mammalian cells via site-specific binding and creation of altered helical structures that provoke DNA repair. However, the use of these molecules for gene targeting requires homopurine tracts to facilitate triple helix formation. Alternatively, to achieve binding to mixed-sequence target sites for the induced gene correction, we have used pseudo-complementary PNAs (pcPNAs). Due to steric hindrance, pcPNAs are unable to form pcPNA–pcPNA duplexes but can bind to complementary DNA sequences via double duplex-invasion complexes. We demonstrate here that pcPNAs, when co-transfected with donor DNA fragments, can promote single base pair modification at the start of the second intron of the beta-globin gene. This was detected by the restoration of proper splicing of transcripts produced from a green fluorescent protein-beta globin fusion gene. We also demonstrate that pcPNAs are effective in stimulating recombination in human fibroblast cells in a manner dependent on the nucleotide excision repair factor, XPA. These results suggest that pcPNAs can be effective tools to induce heritable, site-specific modification of disease-related genes in human cells without purine sequence restriction.

Triplex-stimulated intermolecular recombination at a single-copy genomic target

Gene targeting via homologous recombination offers a potential strategy for therapeutic correction of mutations in disease-related human genes. However, there is a need to improve the efficiency of site-specific recombination by transfected donor DNAs. Oligonucleotide-mediated triple helix formation has been shown to constitute a DNA lesion sufficient to provoke DNA repair and thereby stimulate recombination. However, the ability of triplex-forming oligonucleotides (TFOs) to induce recombination between a target locus and a donor DNA has so far been demonstrated only with multicopy episomal targets in mammalian cells. Using cell lines containing the firefly luciferase reporter gene, we have now established the ability of TFOs to induce gene correction by exogenous donor DNAs at a single-copy chromosomal locus. We find that cotransfection of TFOs and short, single-stranded DNA donor molecules into mammalian cells yields gene correction in a dose-dependent manner at frequencies up to 0.1%, which is five- to ninefold above background. We demonstrate both oligonucleotide-specific and target site-specific effects. We also find that recombination can be induced by both parallel and antiparallel triple helix formation. These results provide further support for the development of TFOs as reagents to stimulate site-specific correction of defective human genes.

Distance and affinity dependence of triplex-induced recombination

Triplex-forming oligonucleotides (TFOs) have the potential to serve as gene therapeutic agents on the basis of their ability to mediate site-specific genome modification via induced recombination. However, high-affinity triplex formation is limited to polypurine/polypyrimidine sites in duplex DNA. Because of this sequence restriction, careful analysis is needed to identify suitable TFO target sites within or near genes of interest. We report here an examination of two key parameters which influence the efficiency of TFO-induced recombination: (1) binding affinity of the TFO for the target site and (2) the distance between the target site and the mutation to be corrected. To test the influence of binding affinity, we compared induced recombination in human cell-free extracts by a series of G-rich oligonucleotides with an identical base composition and an increasing number of mismatches in the third strand binding code. As the number of mismatches increased and, therefore, binding affinity decreased, induced recombination frequency also dropped. There was an apparent threshold at an equilibrium dissociation constant (K(d)) of 1 x 10(-)(7) M. In addition, TFO chemical modification with N,N-diethylethylenediamine (DEED) internucleoside linkages to confer improved binding was found to yield increased levels of induced recombination. To test the ability of triplex formation to induce recombination at a distance, episomal targets with informative reporter genes were constructed to contain polypurine TFO target sites at varying distances from the mutations to be corrected. TFO-induced recombination in mammalian cells between a plasmid vector and a donor oligonucleotide was detected at distances ranging from 24 to 750 bp. Together, these results indicate that TFO-induced recombination requires high-affinity binding but can affect sites hundreds of base pairs away from the position of triplex formation.

Triplex forming oligonucleotides: sequence-specific tools for gene targeting

Sequence-specificity is the key to effective genetic targeting. With specificity, targeted genes can be manipulated in multiple ways; without it, gene therapy agents become loose canons within cells. Triplex forming oligonucleotides (TFOs) bind in the major groove of duplex DNA with high specificity and affinity. Because of these characteristics, TFOs have been proposed as homing devices for genetic manipulation in vivo. Here we review work demonstrating the ability of TFOs and related molecules to alter gene expression and mediate genome modification in mammalian cells. Recent studies have established that TFOs can mediate targeted gene knock out in mice, laying the foundation for the potential application of these molecules in human gene therapy.

A more powerful method to evaluate p-values in GENEHUNTER

The determination of statistical significance in genetic linkage studies is complicated by many factors, such as missing individuals or uninformative markers, and the validity of theoretical results is often questionable. Although many simulation-based methods have been proposed to determine empirically the statistical significance, they are either not generally applicable to complex pedigree structures, or not able to preserve the observed genetic information content at each locus in the pedigrees. We have developed and implemented a general and computationally efficient randomization procedure in GENEHUNTER that applies to arbitrary pedigree structure and preserves the observed information content at each locus. We applied this method to the Problem 1 data set of the Genetic Analysis Workshop 11. The performance of this new method was similar to the method implemented in GENEHUNTER-PLUS, and both outperformed the conservative approach in GENEHUNTER.

Analyses of the COGA data set in one ethnic group with examinations of alternative definitions of alcoholism

We used GENEHUNTER and GENEHUNTER-PLUS to search for linkage with the markers in the Collaborative Study on the Genetics of Alcoholism (COGA) data set in a single ethnic group. Analyses of a complex disorder such as alcoholism depend on the definition of affection status. The COGA study provides two definitions of alcoholism (variables ALDX1 and ALDX2). To identify more severely affected alcoholics that might be more homogeneous genetically, we developed two other ways of characterizing subjects as alcohol dependent: (1) by combining the symptom variable values equally into a 24-point scale and (2) by weighting optimally the symptoms and other descriptive variables into a single score using logistic regression. We applied these definitions within a single ethnic group to map alcoholism-related loci. We found two regions on chromosome 1 that have adjacent markers significant at p-values < or = 0.05. ALDX1 provided the highest Z-scores compared to the alternatives.