The molecular basis of lactase persistence: Linking genetics and epigenetics.

Lactase persistence (LP) - the genetic trait that determines the continued expression of the enzyme lactase into adulthood - has undergone recent, rapid positive selection since the advent of animal domestication and dairying in some human populations. While underlying evolutionary explanations have been widely posited and studied, the molecular basis of LP remains less so. This review considers the genetic and epigenetic bases of LP. Multiple single-nucleotide polymorphisms (SNPs) in an LCT enhancer in intron 13 of the neighbouring MCM6 gene are associated with LP. These SNPs alter binding of transcription factors (TFs) and likely prevent age-related increases in methylation in the enhancer, maintaining LCT expression into adulthood to cause LP. However, the complex relationship between the genetics and epigenetics of LP is not fully characterised, and the mode of action of methylation quantitative trait loci (meQTLs) (SNPs affecting methylation) generally remains poorly understood. Here, we examine published LP data to propose a model describing how methylation in the LCT enhancer is prevented in LP adults. We argue that this occurs through altered binding of the TF Oct-1 (encoded by the gene POU2F1) and neighbouring TFs GATA-6 (GATA6), HNF-3A (FOXA1) and c-Ets1 (ETS1) acting in concert. We therefore suggest a plausible new model for LCT downregulation in the context of LP, with wider relevance for future work on the mechanisms of other meQTLs.

Microvascular maturation of the septal capillary layers takes place in parallel to alveolarization in human lungs.

Primary and secondary septa formed during lung development contain a double-layered capillary network. To improve gas exchange, the capillary network is remodeled into a single-layered one, a process that is called microvascular maturation (MVM). It takes place during classical and continued alveolarization. Classical alveolarization is defined as a formation of new septa from immature septa and continued alveolarization as a formation from mature septa. Until now, MVM was never quantitatively evaluated in human lungs. To correlate alveolarization and MVM, and to determine the transition point from classical to continued alveolarization, the degree of MVM was stereologically estimated. In 12 human lungs (0.1-15 yr), the alveolar surface area of immature and mature septa was estimated stereologically by intersection counting. An MVM-quotient (RMVM) was defined as the mature alveolar surface area over total alveolar surface area. The MVM-quotient increased logarithmically over age and showed a biphasic increase similar to alveolarization. It did not reach 100% maturity in these samples. A linear correlation between the MVM-quotient and the logarithm of the number of alveoli was observed. We conclude that MVM increased logarithmically and biphasically in parallel to alveolarization until alveolarization ceased. However, at 2-3 yr of age three-quarters of the alveolar microvasculature are mature. This result may explain a previous postulate that MVM is finished at this age. We hypothesize that as long as alveolarization takes place, MVM will take place in parallel. We propose that the transition from classical to continued alveolarization takes place between the ages of 1-3 yr in humans.NEW & NOTEWORTHY Newly formed alveolar septa contain a double-layered capillary network. To optimize gas exchange, the two layers fuse to a single-layered capillary network during microvascular maturation. Because its timing is unknow in humans, microvascular maturation was stereologically estimated throughout postnatal human lung development. It is shown that maturation of the microvascular and alveolar septa takes place in parallel to alveolarization. At an age of 2-3 yr three-quarters of the septa are mature.

The hazards of genotype imputation in chromosomal regions under selection: A case study using the Lactase gene region.

Although imputation of missing SNP results has been widely used in genetic studies, claims about the quality and usefulness of imputation have outnumbered the few studies that have questioned its limitations. But it is becoming clear that these limitations are real-for example, disease association signals can be missed in regions of LD breakdown. Here, as a case study, using the chromosomal region of the well-known lactase gene, LCT, we address the issue of imputation in the context of variants that have become frequent in a limited number of modern population groups only recently, due to selection. We study SNPs in a 500 bp region covering the enhancer of LCT, and compare imputed genotypes with directly genotyped data. We examine the haplotype pairs of all individuals with discrepant and missing genotypes. We highlight the nonrandom nature of the allelic errors and show that most incorrect imputations and missing data result from long haplotypes that are evolutionarily closely related to those carrying the derived alleles, while some relate to rare and recombinant haplotypes. We conclude that bias of incorrectly imputed and missing genotypes can decrease the accuracy of imputed results substantially.

Transgender and Gender Diverse Fertility Choices: Supporting the Decision-Making Process for Adolescents and Young Adults.

OBJECTIVE: To qualitatively examine the fertility-related decision making process of transgender and gender diverse (TGD) adolescents and young adults (AYAs) and their parents, in the setting of pursing gender affirming treatments. STUDY DESIGN: Twenty-five TGD AYAs and 6 parents of TGD AYAs participated in a focus group or individual semistructured interviews focused on participants' experience learning about the effects of gender affirming treatments on fertility as well as the process of making a fertility preservation decision. Using open coding, data were analyzed in an iterative process identifying emerging themes and relationships. A decisional satisfaction score was collected and/or coded for each participant. RESULTS: Four broad themes related to the decision-making process were identified: (1) Critical steps include awareness, gathering information, and conversations; (2) External constraints limit choices; (3) Expanding the conversation beyond preservation; and (4) Emotional distress, conflict, and decisional satisfaction. Despite reporting emotional distress or conflict during the decision, TGD AYAs and parents of TGD AYAs generally reported a high level of satisfaction with their fertility preservation decision. CONCLUSIONS: There are specific ways health care professionals and family members can support TGD AYAs in their fertility-related decision making process. Decisional satisfaction was common, regardless of whether TGD AYAs chose to pursue fertility preservation or not.

Epidemiologic Features of the Monkeypox Outbreak and the Public Health Response - United States, May 17-October 6, 2022.

On May 17, 2022, the Massachusetts Department of Health announced the first suspected case of monkeypox associated with the global outbreak in a U.S. resident. On May 23, 2022, CDC launched an emergency response (1,2). CDC's emergency response focused on surveillance, laboratory testing, medical countermeasures, and education. Medical countermeasures included rollout of a national JYNNEOS vaccination strategy, Food and Drug Administration (FDA) issuance of an emergency use authorization to allow for intradermal administration of JYNNEOS, and use of tecovirimat for patients with, or at risk for, severe monkeypox. During May 17-October 6, 2022, a total of 26,384 probable and confirmed* U.S. monkeypox cases were reported to CDC. Daily case counts peaked during mid-to-late August. Among 25,001 of 25,569 (98%) cases in adults with information on gender identity,† 23,683 (95%) occurred in cisgender men. Among 13,997 cisgender men with information on recent sexual or close intimate contact,§ 10,440 (75%) reported male-to-male sexual contact (MMSC) ≤21 days preceding symptom onset. Among 21,211 (80%) cases in persons with information on race and ethnicity,¶ 6,879 (32%), 6,628 (31%), and 6,330 (30%) occurred in non-Hispanic Black or African American (Black), Hispanic or Latino (Hispanic), and non-Hispanic White (White) persons, respectively. Among 5,017 (20%) cases in adults with information on HIV infection status, 2,876 (57%) had HIV infection. Prevention efforts, including vaccination, should be prioritized among persons at highest risk within groups most affected by the monkeypox outbreak, including gay, bisexual, and other men who have sex with men (MSM); transgender, nonbinary, and gender-diverse persons; racial and ethnic minority groups; and persons who are immunocompromised, including persons with advanced HIV infection or newly diagnosed HIV infection.

Group-based pharmacogenetic prediction: is it feasible and do current NHS England ethnic classifications provide appropriate data?

Inter-individual variation of drug metabolising enzymes (DMEs) leads to variable efficacy of many drugs and even adverse drug responses. Consequently, it would be desirable to test variants of many DMEs before drug treatment. Inter-ethnic differences in frequency mean that the choice of SNPs to test may vary across population groups. Here we examine the utility of testing representative groups as a way of assessing what variants might be tested. We show that publicly available population information is potentially useful for determining loci for pre-treatment genetic testing, and for determining the most prevalent risk haplotypes in defined groups. However, we also show that the NHS England classifications have limitations for grouping for these purposes, in particular for people of African descent. We conclude: (1) genotyping of hospital patients and people from the hospital catchment area confers no advantage over using samples from appropriate existing ethnic group collections or publicly available data, (2) given the current NHS England Black African grouping, a decision as to whether to test, would have to apply to all patients of recent Black African ancestry to cover reported risk alleles and (3) the current scarcity of available genome and drug effect data from Africans is a problem for both testing and treatment decisions.

Increased Load to Failure in Biceps Tenodesis With All-Suture Suture Anchor Compared With Interference Screw: A Cadaveric Biomechanical Study.

PURPOSE: To compare the biomechanical characteristics of a single radially expanding all-suture anchor with an interference screw for open subpectoral long head of biceps tendon (LHBT) tenodesis. METHODS: Eighteen fresh-frozen matched-pair human cadaveric humeri were used for this biomechanical study. The matched pair humeri were randomly assigned into 2 experimental biceps tenodesis groups: conventional interference screw (CIS) or all-suture suture anchor (ASSA). Open subpectoral LHBT tenodesis was then performed and biomechanical testing was performed using a servohydraulic test frame. A preload of 5 N was applied for 2 minutes before cyclic loading. Displacement was recorded at cycle 300 (D300) and cycle 500 (D500) and at ultimate failure. Data recorded included displacement, load to failure, displacement at failure. Paired t test was used for analysis. RESULTS: Decreased displacement was observed for the CIS group at D300 (1.67 ± 0.57 mm vs 3.35 ± 2.24 mm; P = .04), D500 (2.00 ± 0.76 mm vs 3.87 ± 2.20 mm; P = .04), and at failure (5.17 ± 3.05 mm vs 10.76 ± 2.66 mm; P < .001). Load to failure was lower in CIS specimens (170 ± 24.5 N vs 217.8 ± 51.54 N; P = .02). Failure in each case was tendon pullout for all CIS specimens; in ASSA 6 specimens failed as the suture pulled through the tendon, 2 specimens failed by suture breakage. No difference in stiffness was observed between the 2 groups (CIS = 98.33 ± 22.98 N/m vs ASSA = 75.94 ± 44.83 N/m; P = .20). CONCLUSIONS: Our study found that open subpectoral biceps tenodesis performed with an ASSA construct results in increased load to failure as compared with CIS. However, the CIS did demonstrate decreased displacement as compared to ASSA in this cadaveric biomechanical study. CLINICAL RELEVANCE: ASSA and CIS at time zero provide fixation as indicated by the provider intraoperatively for LHBT tenodesis. ASSA, however, does remove less cortical bone than does CIS and therefore produces a smaller stress riser in the proximal humerus. Further testing as to the integrity of ASSA is warranted to determine the integrity of the tenodesis with cyclical loading.

Adaptation to milking agropastoralism in Chilean goat herders and nutritional benefit of lactase persistence.

The genetic trait of lactase persistence (LP) evolved as an adaptation to milking pastoralism in the Old World and is a well-known example of positive natural selection in humans. However, the specific mechanisms conferring this selective advantage are unknown. To understand the relationship between milk drinking, LP, growth, reproduction, and survival, communities of the Coquimbo Region in Chile, with recent adoption of milking agropastoralism, were used as a model population. DNA samples and data on stature, reproduction, and diet were collected from 451 participants. Lactose tolerance tests were done on 41 of them. The European -13,910*T (rs4988235) was the only LP causative variant found, showing strong association (99.6%) with LP phenotype. Models of associations of inferred LP status and milk consumption, with fertility, mortality, height, and weight were adjusted with measures of ancestry and relatedness to control for population structure. Although we found no statistically significant effect of LP on fertility, a significant effect (P = 0.002) was observed of LP on body mass index (BMI) in males and of BMI on fertility (P = 0.003). These results fail to support a causal relationship between LP and fertility yet suggest the idea of a nutritional advantage of LP. Furthermore, the proportion of European ancestry around the genetic region of -13,910*T is significantly higher (P = 0.008) than the proportion of European ancestry genome-wide, providing evidence of recent positive selection since European-Amerindian admixture. This signature was absent in nonpastoralist Latin American populations, supporting the hypothesis of specific adaptation to milking agropastoralism in the Coquimbo communities.

Hypomethylation of STAT1 and HLA-DRB1 is associated with type-I interferon-dependent HLA-DRB1 expression in lupus CD8+ T cells.

OBJECTIVE: We examined genome-wide DNA methylation changes in CD8+ T cells from patients with lupus and controls and investigated the functional relevance of some of these changes in lupus. METHODS: Genome-wide DNA methylation of lupus and age, sex and ethnicity-matched control CD8+ T cells was measured using the Infinium MethylationEPIC arrays. Measurement of relevant cell subsets was performed via flow cytometry. Gene expression was quantified by qPCR. Inhibiting STAT1 and CIITA was performed using fludarabine and CIITA siRNA, respectively. RESULTS: Lupus CD8+ T cells had 188 hypomethylated CpG sites compared with healthy matched controls. Among the most hypomethylated were sites associated with HLA-DRB1. Genes involved in the type-I interferon response, including STAT1, were also found to be hypomethylated. IFNα upregulated HLA-DRB1 expression on lupus but not control CD8+ T cells. Lupus and control CD8+ T cells significantly increased STAT1 mRNA levels after treatment with IFNα. The expression of CIITA, a key interferon/STAT1 dependent MHC-class II regulator, is induced by IFNα in lupus CD8+ T cells, but not healthy controls. CIITA knockdown and STAT1 inhibition experiments revealed that HLA-DRB1 expression in lupus CD8+ T cells is dependent on CIITA and STAT1 signalling. Coincubation of naïve CD4+ T cells with IFNα-treated CD8+ T cells led to CD4+ T cell activation, determined by increased expression of CD69 and cytokine production, in patients with lupus but not in healthy controls. This can be blocked by neutralising antibodies targeting HLA-DR. CONCLUSIONS: Lupus CD8+ T cells are epigenetically primed to respond to type-I interferon. We describe an HLA-DRB1+ CD8+ T cell subset that can be induced by IFNα in patients with lupus. A possible pathogenic role for CD8+ T cells in lupus that is dependent on a high type-I interferon environment and epigenetic priming warrants further characterisation.

Benefits of Using The Pause after Death in Emergency Departments: A Delphi Study.

OBJECTIVE: The Pause is a short-term, microbreak created by an emergency nurse in 2009. It provides care team members a few seconds of silence to honor a patient who has died while also honoring the efforts of the team. It is used now on four continents as a standard of care. We investigated how it is being used and why. METHODS: We used a modified Delphi methodology with purposive sampling and a descriptive approach. During the three-round Delphi, we created a data display using open, then axial coding to develop a thematic analysis. Member checking and reflexivity exercises were used to build reliability and trustworthiness of findings. RESULTS: We analyzed 21 transcripts. The Pause is reported to be an ongoing practice in at least 23 health systems globally. Key themes such as Benefits, Self-Care, and Support of other Patients were most pertinent in our analysis. CONCLUSION: The Pause is a low-risk, grassroots intervention that can be led by any member of a care team in emergency settings. It offers self-care for the individual and team. It helps emergency providers feel grounded after a death before going to treat another patient. According to our sample, The Pause helps reduce caregiver stress, which may decrease the risk for burnout. Although further research is recommended, we assert that The Pause be used as a standard of care in emergency departments across the United States.

Unbiased Quantitation of Alveolar Type II to Alveolar Type I Cell Transdifferentiation during Repair after Lung Injury in Mice.

The alveolar epithelium consists of squamous alveolar type (AT) I and cuboidal ATII cells. ATI cells cover 95-98% of the alveolar surface, thereby playing a critical role in barrier integrity, and are extremely thin, thus permitting efficient gas exchange. During lung injury, ATI cells die, resulting in increased epithelial permeability. ATII cells re-epithelialize the alveolar surface via proliferation and transdifferentiation into ATI cells. Transdifferentiation is characterized by down-regulation of ATII cell markers, up-regulation of ATI cell markers, and cell spreading, resulting in a change in morphology from cuboidal to squamous, thus restoring normal alveolar architecture and function. The mechanisms underlying ATII to ATI cell transdifferentiation have not been well studied in vivo. A prerequisite for mechanistic investigation is a rigorous, unbiased method to quantitate this process. Here, we used SPCCreERT2;mTmG mice, in which ATII cells and their progeny express green fluorescent protein (GFP), and applied stereologic techniques to measure transdifferentiation during repair after injury induced by LPS. Transdifferentiation was quantitated as the percent of alveolar surface area covered by ATII-derived (GFP+) cells expressing ATI, but not ATII, cell markers. Using this methodology, the time course and magnitude of transdifferentiation during repair was determined. We found that ATI cell loss and epithelial permeability occurred by Day 4, and ATII to ATI cell transdifferentiation began by Day 7 and continued until Day 16. Notably, transdifferentiation and barrier restoration are temporally correlated. This methodology can be applied to investigate the molecular mechanisms underlying transdifferentiation, ultimately revealing novel therapeutic targets to accelerate repair after lung injury.

World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection.

The genetic trait of lactase persistence (LP) is associated with at least five independent functional single nucleotide variants in a regulatory region about 14 kb upstream of the lactase gene [-13910*T (rs4988235), -13907*G (rs41525747), -13915*G (rs41380347), -14009*G (rs869051967) and -14010*C (rs145946881)]. These alleles have been inferred to have spread recently and present-day frequencies have been attributed to positive selection for the ability of adult humans to digest lactose without risk of symptoms of lactose intolerance. One of the inferential approaches used to estimate the level of past selection has been to determine the extent of haplotype homozygosity (EHH) of the sequence surrounding the SNP of interest. We report here new data on the frequencies of the known LP alleles in the 'Old World' and their haplotype lineages. We examine and confirm EHH of each of the LP alleles in relation to their distinct lineages, but also show marked EHH for one of the older haplotypes that does not carry any of the five LP alleles. The region of EHH of this (B) haplotype exactly coincides with a region of suppressed recombination that is detectable in families as well as in population data, and the results show how such suppression may have exaggerated haplotype-based measures of past selection.

Early life allergen and air pollutant exposures alter longitudinal blood immune profiles in infant rhesus monkeys.

Early life is a critical period for the progressive establishment of immunity in response to environmental stimuli; the impact of airborne challenges on this process is not well defined. In a longitudinal fashion, we determined the effect of episodic house dust mite (HDM) aerosol and ozone inhalation, both separately and combined, on peripheral blood immune cell phenotypes and cytokine expression from 4 to 25weeks of age in an infant rhesus monkey model of childhood development. Immune profiles in peripheral blood were compared with lung lavage at 25weeks of age. Independent of exposure, peripheral blood cell counts fluctuated with chronologic age of animals, while IFNγ and IL-4 mRNA levels increased over time in a linear fashion. At 12weeks of age, total WBC, lymphocyte numbers, FoxP3 mRNA and IL-12 mRNA were dramatically reduced relative to earlier time points, but increased to a steady state with age. Exposure effects were observed for monocyte numbers, as well as CCR3, FoxP3, and IL-12 mRNA levels in peripheral blood. Significant differences in cell surface marker and cytokine expression were detected following in vitro HDM or PMA/ionomycin stimulation of PBMC isolated from animals exposed to either HDM or ozone. Lavage revealed a mixed immune phenotype of FoxP3, IFNγ and eosinophilia in association with combined HDM plus ozone exposure, which was not observed in blood. Collectively, our findings show that airborne challenges during postnatal development elicit measureable cell and cytokine changes in peripheral blood over time, but exposure-induced immune profiles are not mirrored in the lung.

Patient Outcomes as a Function of Shoulder Surgeon Volume: A Systematic Review.

PURPOSE: To examine surgical complications, length of stay, surgical time, cost, revision rates, clinical outcomes, current surgical trends. and minimum number of cases in relationship to surgeon volume for shoulder arthroplasty and rotator cuff repair. METHODS: We performed a systematic review of studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. All studies that met inclusion criteria from January 1990 to January 2016 were included. Inclusion criteria included Level IV evidence or greater, contained specific surgeon volume, and were written in or translated into English. Exclusion criteria included non-English manuscripts, abstracts, and review papers. A written protocol was used to extract relevant data and evaluate study results. Data extracted included volume-specific data pertaining to length of stay, operating time, complications, and cost. RESULTS: A total of 10 studies were included. Seven studies evaluated arthroplasty with 88,740 shoulders, and 3 studies evaluated rotator cuff repair with 63,535 shoulders. Variation was seen in how studies defined low- versus high-volume surgeon. For arthroplasty, <5 cases per year met the criteria for a low-volume surgeon and were associated with increased length of stay, longer operating room time, increased in-hospital complications, and increased cost. Mortality was not significantly increased. In rotator cuff surgery, <12 surgeries per year met the criteria for low volume and were associated with increased length of stay, increased operating room time, and increase in reoperation rate. CONCLUSIONS: Our systematic review demonstrates increased surgical complications, length of stay, surgical time, and surgical cost in shoulder arthroplasty and rotator cuff repair when performed by a low-volume shoulder surgeon, which is defined by those performing <5 arthroplasties and/or <12 rotator cuff repairs per year. LEVEL OF EVIDENCE: Level III, systematic review of Level II and III studies.

Saucerization Versus Complete Resection of a Symptomatic Discoid Lateral Meniscus at Short- and Long-term Follow-up: A Systematic Review.

PURPOSE: To evaluate the surgical outcomes of symptomatic discoid menisci after total meniscectomy, saucerization, and suture repair of tears of a discoid meniscus at short- and long-term follow-up. METHODS: A systematic review was conducted using the Pubmed and ScienceDirect databases in adherence with Preferred Reporting Items of Systematic Reviews and Meta-Analysis guidelines. Short- and long-term follow-up were defined as an average follow-up of <4 years and >4 years, respectively. Pooled quantitative synthesis was performed on studies that reported results of total meniscectomy and saucerization in the same study. A systematic review was performed on studies that reported data on saucerization, total meniscectomy, and/or repair. RESULTS: A total of 19 studies for the short term and 22 for the long term were identified that met inclusion criteria for qualitative review. Of these, 4 short-term and 5 long-term studies were included in the quantitative synthesis. No significant differences in Ikeuchi scores are seen in the short-term studies between saucerization and total meniscectomy; however, the long-term studies did find a statistical difference favoring saucerization (P < .001). The differences noted between the preoperative and postoperative Lysholm scores in the short term were 24.1 (95% conflict of interest: 10.25-37.95) in 3 studies and 22.38 (95% conflict of interest: 17.68-27.07) in the 4 long-term studies for saucerization. Suture repair with saucerization versus saucerization without suture repair revealed a statistical difference in only 1 of 5 studies. CONCLUSIONS: Long-term data demonstrate significantly improved patient reported outcomes in favor of saucerization over total meniscectomy. Suture repair of tears of a lateral discoid meniscus does not demonstrate improved outcomes over partial meniscectomy without repair. Considering the cost of repair and lack of demonstrated improvement, based on the limited available data, we do not recommend repair of the abnormal anatomy in a torn lateral discoid meniscus. LEVEL OF EVIDENCE: Level IV, systematic review.

The Effect of the Pucker Sign on Outcomes of Type III Extension Supracondylar Fractures in Children.

BACKGROUND: The pucker sign, also called skin tenting, indicates significant displacement of the supracondylar fracture and can be a cause for alarm. The purpose of this study is to compare a cohort of patients with type III supracondylar fractures presenting with a pucker sign to a group without a pucker sign by evaluating neurovascular injury at presentation, need for open reduction, persistent neurovascular injury, range of motion, and carrying angle at final follow-up. METHODS: A retrospective review was performed for Gartland type III extension type supracondylar fractures. Those with a pucker sign were identified and evaluated. Type III supracondylar fractures with a pucker sign were compared with a similar cohort without a pucker sign. RESULTS: In total, 12 patients with a pucker sign at an average age of 5.2 years were evaluated. A total of 11 patients (92%) had diminished or absent pulses, and 2 (17%) had weakness in the median nerve distribution. Nine (75%) patients in this group were transferred to the university hospital. Average time to surgery was 8.9 hours with an average operating time of 25.1 minutes. Open reduction was not needed in any case. At an average follow-up of 4.7 months no patients had persistent neurovascular compromise. Two patients lacked <5 degrees of extension and 1 lacked 10 degrees of extension. One patient lacked 10 degrees of flexion. No patients had a change in carrying angle difference compared with the contralateral side. No statistical differences were observed between the 2 groups. CONCLUSIONS: Pucker sign, in the context of a supracondylar fracture of the humerus, is a soft tissue defect with potential entrapment of median nerve and brachial artery. At a maximum time of 16 hours from injury to surgery we report excellent outcomes and no long-term complications. Using the techniques of gradual traction, and milking the soft tissue, the pucker sign can be eliminated. Closed reduction and percutaneous pinning were performed in all the cases. LEVEL OF EVIDENCE: Level III-retrospective comparative study.

SMAD Signaling in the Airways of Healthy Rhesus Macaques versus Rhesus Macaques with Asthma Highlights a Relationship Between Inflammation and Bone Morphogenetic Proteins.

Bone morphogenetic protein (BMP) signaling is important for correct lung morphogenesis, and there is evidence of BMP signaling reactivation in lung diseases. However, little is known about BMP signaling patterns in healthy airway homeostasis and inflammatory airway disease and during epithelial repair. In this study, a rhesus macaque (Macaca mulatta) model of allergic airway disease was used to investigate BMP signaling throughout the airways in health, disease, and regeneration. Stereologic quantification of immunofluorescent images was used to determine the expression of BMP receptor (BMPR) Ia and phosphorylated SMAD (pSMAD) 1/5/8 in the airway epithelium. A pSMAD 1/5/8 expression gradient was found along the airways of healthy juvenile rhesus macaques (n = 3, P < 0.005). Membrane-localized BMPRIa expression was also present in the epithelium of the healthy animals. After exposure to house dust mite allergen and ozone, significant down-regulation of nuclear pSMAD 1/5/8 occurs in the epithelium. When the animals were provided with a recovery period in filtered air, proliferating cell nuclear antigen, pSMAD 1/5/8, and membrane-localized BMPRIa expression were significantly increased in the epithelium of conducting airways (P < 0.005). Furthermore, in the asthmatic airways, altered BMPRIa localization was evident. Because of the elevated eosinophil presence in these airways, we investigated the effect of eosinophil-derived proteins on BMPRIa trafficking in epithelial cells. Eosinophil-derived proteins (eosinophil-derived neurotoxin, eosinophil peroxidase, and major basic protein) induced transient nuclear translocation of membrane-bound BMPRIa. This work mapping SMAD signaling in the airways of nonhuman primates highlights a potential mechanistic relationship between inflammatory mediators and BMP signaling and provides evidence that basal expression of the BMP signaling pathway may be important for maintaining healthy airways.

In Vitro Functional Analyses of Infrequent Nucleotide Variants in the Lactase Enhancer Reveal Different Molecular Routes to Increased Lactase Promoter Activity and Lactase Persistence.

The genetic trait that allows intestinal lactase to persist into adulthood in some 35% of humans worldwide operates at the level of transcription, the effect being caused by cis-acting nucleotide changes upstream of the lactase gene (LCT). A single nucleotide substitution, -13910 C>T, the first causal variant to be identified, accounts for lactase persistence over most of Europe. Located in a region shown to have enhancer function in vitro, it causes increased activity of the LCT promoter in Caco-2 cells, and altered transcription factor binding. Three other variants in close proximity, -13907 C>G, -13915 T>C and -14010 G>C, were later shown to behave in a similar manner. Here, we study four further candidate functional variants. Two, -14009 T>G and -14011 C>T, adjacent to the well-studied -14010 G>C variant, also have a clear effect on promoter activity upregulation as assessed by transfection assays, but notably are involved in different molecular interactions. The results for the two other variants (-14028 T>C, -13779 G>C) were suggestive of function, -14028*C showing a clear change in transcription factor binding, but no obvious effect in transfections, while -13779*G showed greater effect in transfections but less on transcription factor binding. Each of the four variants arose on independent haplotypic backgrounds with different geographic distribution.

Refinement in localization and identification of gene regions associated with Crohn disease.

The risk of Crohn disease (CD) has a large genetic component. A recent meta-analysis of 6 genome-wide association studies reported 71 chromosomal intervals but does not account for all of the known genetic contribution. Here, we refine localization of the previously reported intervals and also identify additional CD susceptibility genes using a mapping approach that localizes causal variants based on genetic maps in linkage disequilibrium units (LDU maps). Using 2 of the 6 cohorts, 66 of the 71 previously reported loci are confirmed and more precise location estimates for these intervals are given. We identify 78 additional gene regions that pass genome-wide significance, providing strong evidence for 144 genes. Additionally, 56 nominally significant signals, but with more stringent and precise colocalization, are identified. In total, we provide evidence for 200 gene regions confirming that CD is truly multifactorial and complex in nature. Many identified genes have functions that are compatible with involvement in immune/inflammatory processes and seem to have a large effect in individuals with extra ileal as well as ileal inflammation. The precise locations and the evidence that some genes reflect phenotypic subgroups will help identify functional variants and will lead to greater insight of CD etiology.

Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep.

The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (-13910(∗)T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (-13907(∗)G, rs41525747; -13915(∗)G, rs41380347; -14010(∗)C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, -14009T>G (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the -14009(∗)G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep.