Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project.

BACKGROUND: A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting. METHODS: We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values. RESULTS: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency. CONCLUSIONS: Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.

The p53-Mdm2 interaction and the E3 ligase activity of Mdm2/Mdm4 are conserved from lampreys to humans.

The extant jawless vertebrates, represented by lampreys and hagfish, are the oldest group of vertebrates and provide an interesting genomic evolutionary pivot point between invertebrates and jawed vertebrates. Through genome analysis of one of these jawless vertebrates, the Japanese lamprey (Lethenteron japonicum), we identified all three members of the important p53 transcription factor family--Tp53, Tp63, and Tp73--as well as the Mdm2 and Mdm4 genes. These genes and their products are significant cellular regulators in human cancer, and further examination of their roles in this most distant vertebrate relative sheds light on their origin and coevolution. Their important role in response to DNA damage has been highlighted by the discovery of multiple copies of the Tp53 gene in elephants. Expression of lamprey p53, Mdm2, and Mdm4 proteins in mammalian cells reveals that the p53-Mdm2 interaction and the Mdm2/Mdm4 E3 ligase activity existed in the common ancestor of vertebrates and have been conserved for >500 million years of vertebrate evolution. Lamprey Mdm2 degrades human p53 with great efficiency, but this interaction is not blocked by currently available small molecule inhibitors of the human HDM2 protein, suggesting utility of lamprey Mdm2 in the study of the human p53 signaling pathway.

Peak density of immature nerve cells occurs with high-grade dysplasia in intraductal papillary mucinous neoplasms of the pancreas.

The development of neural structures within tumors is now considered vital for carcinogenesis. However, the time course of this development in human pre-invasive neoplasia has been incompletely described. Therefore, we performed a detailed analysis of nerves across the neoplastic spectrum in resected intraductal papillary mucinous neoplasms (IPMNs) of the pancreas. Histology and multiplexed immunochemistry demonstrated that nerve density increased from low-grade (LG) to high-grade dysplasia (HG) but did not further increase once invasive IPMN (INV IPMN) was present. Higher nerve density correlated with increasing expression of nerve growth factor (NGF) by the tumor cells. Intra-tumoral nerves were immature and lacked markers of sympathetic, parasympathetic, and sensory lineages. Here, we show for the first time the presence of neural precursor cells (NPCs) within the stroma of pancreatic tumors. The density of these doublecortin (DCX)-positive NPCs increased from LG to HG, but not from HG to INV IPMN. We conclude that peak neural density of tumors is reached in high-grade dysplasia (often termed carcinoma in situ) rather than after invasion. These findings suggest that nerve-tumor interactions are important in IPMN progression and may serve as the basis for future mechanistic studies and novel therapeutic modalities. © 2022 The Pathological Society of Great Britain and Ireland.

Microtia Reconstruction: Our Strategies to Improve the Outcomes.

Introduction : Autologous costal cartilage framework placement is currently the gold standard in patients with microtia. In this article, we present the modifications developed by the author, generally following the principles established by Nagata, and discuss the technical details that have led us to achieve consistently stable and good long-term outcomes for auricular reconstruction in microtia. Materials and Methods : A retrospective review of microtia reconstruction performed from 2015 to 2021 was done. Those who underwent primary reconstruction for microtia and with a minimum follow-up of 6 months with documented photographs were included. Those who underwent secondary reconstruction for microtia and those who did not follow-up for a minimum period of 6 months were excluded. Outcomes were assessed with regard to appearance, and durability of the result. Influence of certain changes like delaying reconstruction until 15 years of age, use of nylon for framework fabrication, etc. over the outcome were assessed. Results : Of 11 ears reconstructed at less than 15 years of age, only one patient (9%) had a good long-term outcome, whereas of the 17 ears reconstructed at greater than 15 years of age, nine patients (53%) had a good long-term outcome. In our experience, infections and wire extrusions were the significant events related to severe cartilage resorption. Conclusion : In our experience, delaying the first stage to 15 years or later, using double-armed nylon sutures, and reducing the projection of the third layer of the framework in select cases have helped to improve our outcomes. Second stage of reconstruction can be avoided if patient is satisfied with the projection achieved in the first stage.

Flavonoids improve the stability and function of P23H rhodopsin slowing down the progression of retinitis pigmentosa in mice.

The balanced homeostasis of the G protein-coupled receptor (GPCR), rhodopsin (Rho), is required for vision. Misfolding mutations in Rho cause photoreceptor death, leading to retinitis pigmentosa (RP) and consequently blindness. With no cure currently available, the development of efficient therapy for RP is an urgent need. Pharmacological supplementation with molecular chaperones, including flavonoids, improves stability, folding, and membrane targeting of the RP Rho mutants in vitro. Thus, we hypothesized that flavonoids by binding to P23H Rho and enhancing its conformational stability could mitigate detrimental effects of this mutation on retinal health. In this work, we evaluated the pharmacological potential of two model flavonoids, quercetin and myricetin, by using in silico, in vitro, and in vivo models of P23H Rho. Our computational analysis showed that quercetin could interact within the orthosteric binding pocket of P23H Rho and shift the conformation of its N-terminal loop toward the wild type (WT)-like state. Quercetin added to the NIH-3T3 cells stably expressing P23H Rho increased the stability of this receptor and improved its function. Systemic administration of quercetin to P23H Rho knock-in mice substantially improved retinal morphology and function, which was associated with an increase in levels of Rho and cone opsins. In addition, treatment with quercetin resulted in downregulation of the UPR signaling and oxidative stress-related markers. This study unravels the pharmacological potential of quercetin to slow down the progression of photoreceptor death in Rho-related RP and highlights its prospective as a lead compound to develop a novel therapeutic remedy to counter RP pathology.

Rapid response to the alpha-1 adrenergic agent phenylephrine in the perioperative period is impacted by genomics and ancestry.

The emergence of genomic data in biobanks and health systems offers new ways to derive medically important phenotypes, including acute phenotypes occurring during inpatient clinical care. Here we study the genetic underpinnings of the rapid response to phenylephrine, an α1-adrenergic receptor agonist commonly used to treat hypotension during anesthesia and surgery. We quantified this response by extracting blood pressure (BP) measurements 5 min before and after the administration of phenylephrine. Based on this derived phenotype, we show that systematic differences exist between self-reported ancestry groups: European-Americans (EA; n = 1387) have a significantly higher systolic response to phenylephrine than African-Americans (AA; n = 1217) and Hispanic/Latinos (HA; n = 1713) (31.3% increase, p value < 6e-08 and 22.9% increase, p value < 5e-05 respectively), after adjusting for genetic ancestry, demographics, and relevant clinical covariates. We performed a genome-wide association study to investigate genetic factors underlying individual differences in this derived phenotype. We discovered genome-wide significant association signals in loci and genes previously associated with BP measured in ambulatory settings, and a general enrichment of association in these genes. Finally, we discovered two low frequency variants, present at ~1% in EAs and AAs, respectively, where patients carrying one copy of these variants show no phenylephrine response. This work demonstrates our ability to derive a quantitative phenotype suited for comparative statistics and genome-wide association studies from dense clinical and physiological measures captured for managing patients during surgery. We identify genetic variants underlying non response to phenylephrine, with implications for preemptive pharmacogenomic screening to improve safety during surgery.

The Current UK Consensus on the Management of Weber B and Posterior Ankle Fractures: A Questionnaire Study as Part of the Acute Management of Ankle Fractures (AUGMENT) Audit.

Ankle fractures are common conditions which are associated with significant morbidity when managed incorrectly. With the incidence due to triple by 2030, standards of practice were created by the British Orthopaedic Association and the British Orthopaedic Foot and Ankle Society to ensure optimal treatment. In spite of this, anecdotally there is still a variation in practice and therefore a questionnaire study was designed to explore clinician decision-making around Weber B and Posterior Malleolus ankle fractures. Five scenarios explored management regarding minimally and grossly displaced injuries, as well as the use of further imaging. The questionnaires were distributed via AUGMENT collaborators at their sites and at the British Orthopaedic Foot and Ankle Society congress 2018. About 315 questionnaires were completed and included in analysis. For Weber B injuries, overall there was a consensus across all respondents with minimally displaced and grossly displaced fractures being treated conservatively and operatively respectively. For Posterior Malleolus injuries, there was variation in practice between Foot and Ankle specialists and their non-Foot and Ankle colleagues. Computed tomography (CT) was more likely to be used to assess these injuries by specialists (97.50 vs 69.79%) and these injuries were more likely to be treated operatively across the board. This study identified key variation in practice of the management of Posterior Malleolar ankle fractures, including the use of imaging to further define the anatomy and the decision to operate. Foot and Ankle surgeons were more likely to organize CT scans and to surgically manage these injures.

The regulatory TnaC nascent peptide preferentially inhibits release factor 2-mediated hydrolysis of peptidyl-tRNA.

The tnaC regulatory gene from the tna operon of Escherichia coli controls the transcription of its own operon through an attenuation mechanism relying on the accumulation of arrested ribosomes during inhibition of its own translation termination. This free l-Trp-dependent mechanism of inhibition of translation termination remains unclear. Here, we analyzed the inhibitory effects of l-Trp on the function of two known E. coli translation termination factors, RF1 and RF2. Using a series of reporter genes, we found that the in vivo l-Trp sensitivity of tnaC gene expression is influenced by the identity of its stop codon, with the UGA stop codon producing higher expression efficiency of the tnaA-lacZ gene construct than the UAG stop codon. In vitro TnaC-peptidyl-tRNA accumulation and toe-printing assays confirmed that in the presence of l-Trp, the UGA stop codon generates higher accumulation of both TnaC-peptidyl-tRNA and arrested ribosomes than does the UAG stop codon. RF-mediated hydrolysis assays corroborated that l-Trp blocks RF2 function more than that of RF1. Mutational analyses disclosed that amino acids substitutions at the 246 and 256 residue positions surrounding the RF2-GGQ functional motif reduce l-Trp-dependent expression of the tnaC(UGA) tnaA-lacZ construct and the ability of l-Trp to inhibit RF2-mediated cleavage of the TnaC-peptidyl-tRNA. Altogether, our results indicate that l-Trp preferentially blocks RF2 activity during translation termination of the tnaC gene. This inhibition depends on the identities of amino acid residues surrounding the RF2-GGQ functional motif.

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases.

Whole-genome sequencing (WGS) holds great potential as a diagnostic test. However, the majority of patients currently undergoing WGS lack a molecular diagnosis, largely due to the vast number of undiscovered disease genes and our inability to assess the pathogenicity of most genomic variants. The CAGI SickKids challenges attempted to address this knowledge gap by assessing state-of-the-art methods for clinical phenotype prediction from genomes. CAGI4 and CAGI5 participants were provided with WGS data and clinical descriptions of 25 and 24 undiagnosed patients from the SickKids Genome Clinic Project, respectively. Predictors were asked to identify primary and secondary causal variants. In addition, for CAGI5, groups had to match each genome to one of three disorder categories (neurologic, ophthalmologic, and connective), and separately to each patient. The performance of matching genomes to categories was no better than random but two groups performed significantly better than chance in matching genomes to patients. Two of the ten variants proposed by two groups in CAGI4 were deemed to be diagnostic, and several proposed pathogenic variants in CAGI5 are good candidates for phenotype expansion. We discuss implications for improving in silico assessment of genomic variants and identifying new disease genes.

Discovering Putative Protein Targets of Small Molecules: A Study of the p53 Activator Nutlin.

Small molecule drugs bind to a pocket in disease causing target proteins based on complementarity in shape and physicochemical properties. There is a likelihood that other proteins could have binding sites that are structurally similar to the target protein. Binding to these other proteins could alter their activities leading to off target effects of the drug. One such small molecule drug Nutlin binds the protein MDM2, which is upregulated in several types of cancer and is a negative regulator of the tumor suppressor protein p53. To investigate the off target effects of Nutlin, we present here a shape-based data mining effort. We extracted the binding pocket of Nutlin from the crystal structure of Nutlin bound MDM2. We next mined the protein structural database (PDB) for putative binding pockets in other human protein structures that were similar in shape to the Nutlin pocket in MDM2 using our topology-independent structural superimposition tool CLICK. We detected 49 proteins which have binding pockets that were structurally similar to the Nutlin binding site of MDM2. All of the potential complexes were evaluated using molecular mechanics and AutoDock Vina docking scores. Further, molecular dynamics simulations were carried out on four of the predicted Nutlin-protein complexes. The binding of Nutlin to one of these proteins, gamma glutamyl hydrolase, was also experimentally validated by a thermal shift assay. These findings provide a platform for identifying potential off-target effects of existing/new drugs and also opens the possibilities for repurposing drugs/ligands.

Preoperative QTc Interval is Not Associated With Intraoperative Cardiac Events or Mortality in Liver Transplantation Patients.

OBJECTIVES: The primary objective of this study was to determine whether liver transplantation recipients with preoperative prolonged corrected (QTc) intervals have a higher incidence of intraoperative cardiac events and/or postoperative mortality compared with their peers with normal QTc intervals. DESIGN: This was a retrospective cohort study. SETTING: Single academic hospital in New York, NY. PARTICIPANTS: Patients undergoing liver transplantation between 2007 and 2016. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Data relating to all liver transplantation recipients with preoperative electrocardiograms were queried from an institutional anesthesia data warehouse and electronic medical records. Primary outcomes were a composite outcome of intraoperative cardiac events and postoperative mortality. Patients with a prolonged QTc interval (>450 ms for men, >470 ms for women) did not demonstrate an association with intraoperative cardiac events, 30- or 90-day mortality, in-hospital mortality, or overall mortality compared with recipients in the normal QTc interval group. A prolonged QTc was found to be associated with increased anesthesia time, surgical time, length of hospital stay, and incidence of fresh frozen plasma and platelets transfusion. CONCLUSIONS: Prolonged QTc interval is not associated with an increased incidence of intraoperative cardiac events or mortality in liver transplantation recipients. The demonstrated correlation among QTc length and Model for End-stage Liver Disease score, blood component requirements, surgical and anesthetic times, and hospital length of stay likely represents the association between QTc length and severity of liver disease.

An Automated Critical Event Screening and Notification System to Facilitate Preanesthesia Record Review.

BACKGROUND: Anesthesia information management systems make prior anesthesia records readily available for review when patients return for a subsequent procedure but may create a problem of too much documentation to review in a limited amount of time. We implemented a screening tool to facilitate the identification of critical documentation for review. METHODS: An algorithm was developed to electronically search prior anesthesia records for predefined critical events and flag records containing these events. Our web-based daily case schedule was modified to contain a warning message for any patient on the schedule who has a prior record flagged by the system, in addition to a preexisting hyperlink to view the relevant record. A retrospective analysis was performed to determine the impact of the warning messages on the frequency with which the care team reviewed these records before providing anesthesia care. RESULTS: The screening algorithm flagged 13% of archived cases as critical. There were 3329 and 3369 cases in the 6 months before and after system implementation, respectively, that had prior critical records available for review at that time. One or more of these critical records were viewed before the subsequent case start in 39% vs 59% (P < .01) of cases in the pre- versus postimplementation periods. Subgroup analysis revealed that the increase was greatest for attending anesthesiologists working alone. CONCLUSIONS: We created a system to automatically detect critical events in prior anesthesia records for the purpose of forewarning the anesthesia care team when the same patient returns for another procedure. Inclusion of these warnings on the daily case schedule was associated with an increased frequency of preanesthesia review of old records.

Multispot launching for single-mode excitation in multimode fibers for high-speed applications.

Several launching methods have been employed in multimode fibers (MMFs) to reduce the intermodal dispersion. Selective excitation of the fundamental mode alone in an MMF can eliminate intermodal dispersion completely, provided the mode coupling along the fiber is minimum. In this paper, we present the design of a two-core fiber taper that results in the generation of a mode-field diameter-matched twin-spot beam, which can effectively excite only the fundamental mode (LP01) in an MMF. We also propose a new launching method, viz. dual twin-spot launching, which excites the LP01 mode alone in an MMF for a wide range of input beam spot sizes as compared to the other existing methods. The design of a four-core fiber taper for generating the proposed dual twin-spot beam is also presented. Misalignment tolerance of the dual twin-spot beam launching is compared with mode-field diameter-matched center launch (MFDM-CL) and mode-field diameter-matched twin-spot launch (MFDM-TSL). We show that the dual twin-spot launching method has higher alignment tolerances.

Demographic and Practice Characteristics of Physicians Who Care for Medically Underserved People: A National Survey.

OBJECTIVES: Few national studies have examined the influence of role models as a potential predictor for caring for medically underserved (MUS) patients. This study tested associations between previous physician role model exposure and caring for MUS populations, as well as examines the practice environments of these physicians. METHODS: Between October and December 2011, we mailed a confidential questionnaire to a representative sample of 2000 US physicians from various specialties. The primary criterion variable was "Is your patient population considered medically underserved?" We assessed demographic and other personal characteristics (calling, spirituality, and reporting a familial role model). We also asked about their practice characteristics, including a validated measure that assessed whether their work environment was considered chaotic/hectic or calm. RESULTS: The survey response rate was 64.5% (1289/2000). Female physicians and African American physicians were more likely to report working in MUS settings (multivariate odds ratio [OR] 1.32, confidence interval [CI] 1.00-1.76 and OR 2.65, CI 1.28-5.46, respectively). Physicians with high spirituality (OR 1.69, CI 1.02-2.79) and who reported familial role model exposure (OR 1.91, CI 1.11-3.30) also were associated with working with MUS populations. Physicians who worked in academic medical centers (OR 1.93, CI 1.45-2.56) and in chaotic work environments (OR 3.25, CI 1.64-6.44) also were more likely to report working with MUS patients. CONCLUSIONS: Familial role models may be influencing physicians to work with MUS patients, but the quality of their current work environments raises concerns about the long-term retention of physicians in MUS settings.

iGAS: A framework for using electronic intraoperative medical records for genomic discovery.

OBJECTIVE: Design and implement a HIPAA and Integrating the Healthcare Enterprise (IHE) profile compliant automated pipeline, the integrated Genomics Anesthesia System (iGAS), linking genomic data from the Mount Sinai Health System (MSHS) BioMe biobank to electronic anesthesia records, including physiological data collected during the perioperative period. The resulting repository of multi-dimensional data can be used for precision medicine analysis of physiological readouts, acute medical conditions, and adverse events that can occur during surgery. MATERIALS AND METHODS: A structured pipeline was developed atop our existing anesthesia data warehouse using open-source tools. The pipeline is automated using scheduled tasks. The pipeline runs weekly, and finds and identifies all new and existing anesthetic records for BioMe participants. RESULTS: The pipeline went live in June 2015 with 49.2% (n=15,673) of BioMe participants linked to 40,947 anesthetics. The pipeline runs weekly in minimal time. After eighteen months, an additional 3671 participants were enrolled in BioMe and the number of matched anesthetic records grew 21% to 49,545. Overall percentage of BioMe patients with anesthetics remained similar at 51.1% (n=18,128). Seven patients opted out during this time. The median number of anesthetics per participant was 2 (range 1-144). Collectively, there were over 35 million physiologic data points and 480,000 medication administrations linked to genomic data. To date, two projects are using the pipeline at MSHS. CONCLUSION: Automated integration of biobank and anesthetic data sources is feasible and practical. This integration enables large-scale genomic analyses that might inform variable physiological response to anesthetic and surgical stress, and examine genetic factors underlying adverse outcomes during and after surgery.

Modified twin-spot launching: an improved launching technique for enhancing data rates in multimode fiber.

Several launching techniques, such as center launching, offset launching, mode-field diameter-matched center launching, twin-spot launching, etc., have been employed in the past to reduce modal dispersion in multimode fibers (MMFs). Unfortunately, all these methods require stringent alignment accuracy of an input beam with the fiber axis. In this paper, we propose a new optical launching method, viz., the mode-field diameter-matched twin-spot launching technique, which combines the desirable features of two earlier techniques so as to excite only the fundamental mode in an MMF with much higher misalignment tolerance compared to existing launching techniques. Also, we derive for the first time an analytical expression for power coupling coefficients of the excited modes in an infinite parabolic refractive index profiled MMF under twin-spot launching. The proposed technique can excite the fundamental mode with more than 9 dB extinction ratio at 1300 nm, even though the two beams are at a lateral offset position of 5 µm from the axis (i.e., 10 µm apart). Additionally, it is tolerant of variations in the mode-field diameter, relative positions, power, and phase of the input beams. The comprehensive analysis shows cancellation of the odd/even symmetrical mode groups in an MMF depending on the relative phase of the input beams that results in reduced group-delay differences of the excited mode groups.

A Retrospective Study of Success, Failure, and Time Needed to Perform Awake Intubation.

BACKGROUND: Awake intubation is the standard of care for management of the anticipated difficult airway. The performance of awake intubation may be perceived as complex and time-consuming, potentially leading clinicians to avoid this technique of airway management. This retrospective review of awake intubations at a large academic medical center was performed to determine the average time taken to perform awake intubation, its effects on hemodynamics, and the incidence and characteristics of complications and failure. METHODS: Anesthetic records from 2007 to 2014 were queried for the performance of an awake intubation. Of the 1,085 awake intubations included for analysis, 1,055 involved the use of a flexible bronchoscope. Each awake intubation case was propensity matched with two controls (1:2 ratio), with similar comorbidities and intubations performed after the induction of anesthesia (n = 2,170). The time from entry into the operating room until intubation was compared between groups. The anesthetic records of all patients undergoing awake intubation were also reviewed for failure and complications. RESULTS: The median time to intubation for patients intubated post induction was 16.0 min (interquartile range: 13 to 22) from entrance into the operating room. The median time to intubation for awake patients was 24.0 min (interquartile range: 19 to 31). The complication rate was 1.6% (17 of 1,085 cases). The most frequent complications observed were mucous plug, endotracheal tube cuff leak, and inadvertent extubation. The failure rate for attempted awake intubation was 1% (n = 10). CONCLUSIONS: Awake intubations have a high rate of success and low rate of serious complications and failure. Awake intubations can be performed safely and rapidly.

The Role of Oligosaccharides in Host-Microbial Interactions for Human Health.

Milk oligosaccharides have many associated bioactivities which can contribute to human health and offer protective properties to the host. Such bioactivities include anti-infective properties whereby oligosaccharides interact with bacterial cells and prevent adhesion to the host and subsequent colonization. Milk oligosaccharides have also been shown to alter the glycosylation of intestinal cells, leading to a reduction in pathogenic colonization. In addition, these sugars promote adhesion of commensal bacterial strains to host cells as well as possessing the ability to alter mucin expression in intestinal cells and improve barrier function. The ability of milk oligosaccharides to alter the transcriptome of both commensal bacterial strains and intestinal epithelial cells has also been revealed, indicating the potential of many cell types to detect the presence of milk oligosaccharides and respond accordingly at the genetic level. Interestingly, domestic animal milk may provide a bioactive source of oligosaccharides for formula supplementation with the aim of emulating the gold standard that is human milk. Overall, this review highlights the ability of milk oligosaccharides to promote health in a variety of ways, for example, through direct bacterial interactions, immunomodulatory activities, promotion of gut barrier function, and induction of protective transcriptional responses.