Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors.

Analyzing single-cell transcriptomes promises to decipher the plasticity, heterogeneity, and rapid switches in developmental cellular state transitions. Such analyses require the identification of gene markers for semi-stable transition states. However, there are nontrivial challenges such as unexplainable stochasticity, variable population sizes, and alternative trajectory constructions. By advancing current tipping-point theory-based models with feature selection, network decomposition, accurate estimation of correlations, and optimization, we developed BioTIP to overcome these challenges. BioTIP identifies a small group of genes, called critical transition signal (CTS), to characterize regulated stochasticity during semi-stable transitions. Although methods rooted in different theories converged at the same transition events in two benchmark datasets, BioTIP is unique in inferring lineage-determining transcription factors governing critical transition. Applying BioTIP to mouse gastrulation data, we identify multiple CTSs from one dataset and validated their significance in another independent dataset. We detect the established regulator Etv2 whose expression change drives the haemato-endothelial bifurcation, and its targets together in CTS across three datasets. After comparing to three current methods using six datasets, we show that BioTIP is accurate, user-friendly, independent of pseudo-temporal trajectory, and captures significantly interconnected and reproducible CTSs. We expect BioTIP to provide great insight into dynamic regulations of lineage-determining factors.

Atypical Wenckebach without grouped beating due to dual AV nodal conduction.

A 31-year-old woman reported dizziness in the early postpartum period after receiving dexmedetomidine. The ECG was misinterpreted as complete heart block; however, more careful analysis revealed an atypical Wenckebach pattern with dual AV nodal conduction and termination of nonconducted P waves with junctional escape beats. The patient's rhythm returned to sinus after stopping dexmedetomidine. Atypical Wenckebach patterns account for greater than 50% of patients with Mobitz Type I AV block and can be misinterpreted as high-grade AV block. This case highlights the causes of atypical Wenckebach patterns and how careful analysis of intervals can help clinicians avoid misdiagnosis.

CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs.

Motivation: Long intergenic noncoding RNAs (lincRNAs) have risen to prominence in cancer biology as new biomarkers of disease. Those lincRNAs transcribed from active cis-regulatory elements (enhancers) have provided mechanistic insight into cis-acting regulation; however, in the absence of an enhancer hallmark, computational prediction of cis-acting transcription of lincRNAs remains challenging. Here, we introduce a novel transcriptomic method: a cis-regulatory lincRNA-gene associating metric, termed 'CisPi'. CisPi quantifies the mutual information between lincRNAs and local gene expression regarding their response to perturbation, such as disease risk-dependence. To predict risk-dependent lincRNAs in neuroblastoma, an aggressive pediatric cancer, we advance this scoring scheme to measure lincRNAs that represent the minority of reads in RNA-Seq libraries by a novel side-by-side analytical pipeline. Results: Altered expression of lincRNAs that stratifies tumor risk is an informative readout of oncogenic enhancer activity. Our CisPi metric therefore provides a powerful computational model to identify enhancer-templated RNAs (eRNAs), eRNA-like lincRNAs, or active enhancers that regulate the expression of local genes. First, risk-dependent lincRNAs revealed active enhancers, over-represented neuroblastoma susceptibility loci, and uncovered novel clinical biomarkers. Second, the prioritized lincRNAs were significantly prognostic. Third, the predicted target genes further inherited the prognostic significance of these lincRNAs. In sum, RNA-Seq alone is sufficient to identify disease-associated lincRNAs using our methodologies, allowing broader applications to contexts in which enhancer hallmarks are not available or show limited sensitivity. Availability and implementation: The source code is available on request. The prioritized lincRNAs and their target genes are in the Supplementary Material. Supplementary information: Supplementary data are available at Bioinformatics online.

Immune Reconstitution Following Autologous Stem Cell Transplantation in Patients with High-Risk Neuroblastoma at the Time of Immunotherapy.

Outcomes for patients with high-risk neuroblastoma (HR-NBL) are significantly improved with the addition of immunotherapy (dinutuximab + cytokines) following autologous hematopoietic stem cell transplantation (auto-HSCT). We hypothesized that the immune system is not fully reconstituted at the initiation of immunotherapy. To test this hypothesis, we evaluated hematologic and immune subsets in 34 patients with HR-NBL before and after auto-HSCT. We found that absolute T, B, and NK cell counts at the time of immunotherapy were below normal in 80% of patients. Patients with residual disease at the time of transplantation had significantly lower absolute lymphocyte counts (ALC; P = .008), lower CD16+ cell counts (P = .009), and an abnormal ratio of cytokine-releasing to cytotoxic NK cells at the time of dinutuximab treatment. In addition, the preparative regimen used for auto-HSCT predicted immune recovery. Finally, higher total white blood cell count (P = .013) and ALC (P = .013) at 3 months after completion of therapy were measured in patients who remained in remission compared with those who relapsed. Our results indicate that most patients with HR-NBL do not have full immune reconstitution at the time of dinutuximab treatment after auto-HSCT, and that immune recovery may correlate with disease-related outcomes in patients with high-risk disease.

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.

UNLABELLED: Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements. AVAILABILITY AND IMPLEMENTATION: The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html. CONTACT: xyang2@uchicago.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia.

BACKGROUND: Genes that regulate stem cell function are suspected to exert adverse effects on prognosis in malignancy. However, diverse cancer stem cell signatures are difficult for physicians to interpret and apply clinically. To connect the transcriptome and stem cell biology, with potential clinical applications, we propose a novel computational "gene-to-function, snapshot-to-dynamics, and biology-to-clinic" framework to uncover core functional gene-sets signatures. This framework incorporates three function-centric gene-set analysis strategies: a meta-analysis of both microarray and RNA-seq data, novel dynamic network mechanism (DNM) identification, and a personalized prognostic indicator analysis. This work uses complex disease acute myeloid leukemia (AML) as a research platform. RESULTS: We introduced an adjustable "soft threshold" to a functional gene-set algorithm and found that two different analysis methods identified distinct gene-set signatures from the same samples. We identified a 30-gene cluster that characterizes leukemic stem cell (LSC)-depleted cells and a 25-gene cluster that characterizes LSC-enriched cells in parallel; both mark favorable-prognosis in AML. Genes within each signature significantly share common biological processes and/or molecular functions (empirical p = 6e-5 and 0.03 respectively). The 25-gene signature reflects the abnormal development of stem cells in AML, such as AURKA over-expression. We subsequently determined that the clinical relevance of both signatures is independent of known clinical risk classifications in 214 patients with cytogenetically normal AML. We successfully validated the prognosis of both signatures in two independent cohorts of 91 and 242 patients respectively (log-rank p < 0.0015 and 0.05; empirical p < 0.015 and 0.08). CONCLUSION: The proposed algorithms and computational framework will harness systems biology research because they efficiently translate gene-sets (rather than single genes) into biological discoveries about AML and other complex diseases.

CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia.

Loss of chromosome 7 and del(7q) [-7/del(7q)] are recurring cytogenetic abnormalities in hematologic malignancies, including acute myeloid leukemia and therapy-related myeloid neoplasms, and associated with an adverse prognosis. Despite intensive effort by many laboratories, the putative myeloid tumor suppressor(s) on chromosome 7 has not yet been identified.We performed transcriptome sequencing and SNP array analysis on de novo and therapy-related myeloid neoplasms, half with -7/del(7q). We identified a 2.17-Mb commonly deleted segment on chromosome band 7q22.1 containing CUX1, a gene encoding a homeodomain-containing transcription factor. In 1 case, CUX1 was disrupted by a translocation, resulting in a loss-of-function RNA fusion transcript. CUX1 was the most significantly differentially expressed gene within the commonly deleted segment and was expressed at haploinsufficient levels in -7/del(7q) leukemias. Haploinsufficiency of the highly conserved ortholog, cut, led to hemocyte overgrowth and tumor formation in Drosophila melanogaster. Similarly, haploinsufficiency of CUX1 gave human hematopoietic cells a significant engraftment advantage on transplantation into immunodeficient mice. Within the RNA-sequencing data, we identified a CUX1-associated cell cycle transcriptional gene signature, suggesting that CUX1 exerts tumor suppressor activity by regulating proliferative genes. These data identify CUX1 as a conserved, haploinsufficient tumor suppressor frequently deleted in myeloid neoplasms.

Adenovirus-associated virus vector-mediated gene transfer in hemophilia B.

BACKGROUND: Hemophilia B, an X-linked disorder, is ideally suited for gene therapy. We investigated the use of a new gene therapy in patients with the disorder. METHODS: We infused a single dose of a serotype-8-pseudotyped, self-complementary adenovirus-associated virus (AAV) vector expressing a codon-optimized human factor IX (FIX) transgene (scAAV2/8-LP1-hFIXco) in a peripheral vein in six patients with severe hemophilia B (FIX activity, <1% of normal values). Study participants were enrolled sequentially in one of three cohorts (given a high, intermediate, or low dose of vector), with two participants in each group. Vector was administered without immunosuppressive therapy, and participants were followed for 6 to 16 months. RESULTS: AAV-mediated expression of FIX at 2 to 11% of normal levels was observed in all participants. Four of the six discontinued FIX prophylaxis and remained free of spontaneous hemorrhage; in the other two, the interval between prophylactic injections was increased. Of the two participants who received the high dose of vector, one had a transient, asymptomatic elevation of serum aminotransferase levels, which was associated with the detection of AAV8-capsid-specific T cells in the peripheral blood; the other had a slight increase in liver-enzyme levels, the cause of which was less clear. Each of these two participants received a short course of glucocorticoid therapy, which rapidly normalized aminotransferase levels and maintained FIX levels in the range of 3 to 11% of normal values. CONCLUSIONS: Peripheral-vein infusion of scAAV2/8-LP1-hFIXco resulted in FIX transgene expression at levels sufficient to improve the bleeding phenotype, with few side effects. Although immune-mediated clearance of AAV-transduced hepatocytes remains a concern, this process may be controlled with a short course of glucocorticoids without loss of transgene expression. (Funded by the Medical Research Council and others; ClinicalTrials.gov number, NCT00979238.).

Social Determinants of Health Impacting the Experience of Young Adults With Cancer at a Single Community Urban Hospital: A Retrospective Cohort Study.

Adolescent and young adult (AYA) cancer patients receive palliative medicine consultation at a late stage and face diagnostic delays. Failure to address social determinants of health (SDOH) and AYA-specific needs can adversely impact patient experience. This retrospective observational cohort study used data from chart review to assess the frequency of SDOH impacting AYA patients and setting of initial diagnosis at a US urban safety-net hospital. The association of SDOH variables with delays in treatment, loss of follow-up, and no-shows was tested using Chi-square and t-tests. One hundred seventy five patient charts were reviewed. Sixty-two percent were diagnosed in acute care settings. Substance use disorders, financial, employment, and insurance issues were associated with delayed treatment, with weak to moderate effect sizes. Mental health diagnoses, substance use disorder, homelessness, and financial burdens were associated with patient no-shows, with moderate to large effect sizes. Twenty-five percent of patients received palliative medicine consultation; 70% of these occurred at end of life. This study demonstrates the impact of SDOH on AYA cancer care and the need for policy allowing for intervention on SDOH.

The spacing effect: Improving electrocardiogram interpretation.

BACKGROUND: Accurate electrocardiogram (ECG) interpretation is critical for safe patient care, making this skill a necessary competency for medical school graduation. Improved long-term memory retention with repeated exposure to material is one of the most evidenced-based components of adult learning science. This curricular innovation aimed to determine if implementing spaced repetition and retrieval practice using ECG quizzes during the principal clinical year would improve ECG interpretation skills among medical students enrolled in a Longitudinal Integrated Clerkship (LIC). APPROACH: The curricular innovation applied the spacing effect and retrieval practice. Cognitive science demonstrates enhanced long-term retention through repeated interval exposure to learned material. Studies of spaced retrieval indicate that memory retention is enhanced through tests involving effortful recall. LIC students in an intervention group were exposed to the spacing effect with periodic ECG quizzes throughout their clinical clerkship year. EVALUATION: The results of the 17-item post-test for 140 students were analysed: LIC intervention, N = 54; block control, N = 62; and LIC control, N = 24. The ANOVA test was significant (p < 0.001). Games-Howell post hoc testing showed that the mean score in the LIC intervention group was significantly higher compared with the LIC control group (p < 0.001) and the block control group (p < 0.001). There was no significant difference between the LIC control and block control groups (p = 0.59). IMPLICATIONS: Spaced repetition of material through ECG quizzes improved ECG interpretation skills on an ECG post-test and mitigates the forgetting curve, maintaining student competency in ECG interpretation.

Preliminary Workforce Outcomes of an Urban Longitudinal Integrated Clerkship.

PURPOSE: The authors examined whether students participating in an urban longitudinal integrated clerkship (LIC) with a curriculum focused on care for underserved populations have a sustained commitment to urban underserved care through residency training and into practice. METHOD: This mixed-methods study collected data from medical student application essays to the Denver Health LIC (DH-LIC), end-of-course surveys, residency match outcomes, and postgraduation surveys annually for academic years 2014 to 2022. The authors analyzed students' responses to the surveys on interest in working with underserved patients, understanding the rewards and challenges of working in safety net institutions, working in the community to improve health, and working at DH. The authors qualitatively coded the 70 application essays of all selected students using summative content analysis. RESULTS: Seventy DH-LIC students were compared with 1,450 medical students between 2014 and 2022. Qualitative analysis of LIC application essays revealed 3 themes: interest in working with underserved populations, work experience with underserved populations, and personal experience with medical vulnerability. Fifty-seven DH-LIC participants (81.4%) expressed high levels of career interest in working with underserved populations, 45 (64.3%) had high levels of work experience with underserved populations, and 18 (25.7%) expressed high levels of personal experience. Graduates of the DH-LIC program demonstrated a high degree of continuing interest in practicing in urban underserved settings throughout medical school and postgraduate training. Ten graduates (71.4%) in practice work in urban underserved settings. Participants reported a high or very high level of interest and commitment to working with underserved populations (96.7%-100%), understanding the safety net health care system (91.7%-98.6%), and working in communities (95.0%-100%) at all time points studied. CONCLUSIONS: Early data indicate high rates of graduates working in urban underserved settings. These preliminary outcomes suggest the LIC may support the development of a committed workforce for urban underserved communities.

ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment.

Mechanisms underlying distinct specification, commitment, and differentiation phases of cell fate determination remain undefined due to difficulties capturing these processes. Here, we interrogate the activity of ETV2, a transcription factor necessary and sufficient for hematoendothelial differentiation, within isolated fate intermediates. We observe transcriptional upregulation of Etv2 and opening of ETV2-binding sites, indicating new ETV2 binding, in a common cardiac-hematoendothelial progenitor population. Accessible ETV2-binding sites are active at the Etv2 locus but not at other hematoendothelial regulator genes. Hematoendothelial commitment coincides with the activation of a small repertoire of previously accessible ETV2-binding sites at hematoendothelial regulators. Hematoendothelial differentiation accompanies activation of a large repertoire of new ETV2-binding sites and upregulation of hematopoietic and endothelial gene regulatory networks. This work distinguishes specification, commitment, and sublineage differentiation phases of ETV2-dependent transcription and suggests that the shift from ETV2 binding to ETV2-bound enhancer activation, not ETV2 binding to target enhancers, drives hematoendothelial fate commitment.

Perturbed desmosomal cadherin expression in grainy head-like 1-null mice.

In Drosophila, the grainy head (grh) gene plays a range of key developmental roles through the regulation of members of the cadherin gene family. We now report that mice lacking the grh homologue grainy head-like 1 (Grhl1) exhibit hair and skin phenotypes consistent with a reduction in expression of the genes encoding the desmosomal cadherin, desmoglein 1 (Dsg1). Grhl1-null mice show an initial delay in coat growth, and older mice exhibit hair loss as a result of poor anchoring of the hair shaft in the follicle. The mice also develop palmoplantar keratoderma, analogous to humans with DSG1 mutations. Sequence analysis, DNA binding, and chromatin immunoprecipitation experiments demonstrate that the human and mouse Dsg1 promoters are direct targets of GRHL1. Ultrastructural analysis reveals reduced numbers of abnormal desmosomes in the interfollicular epidermis. These findings establish GRHL1 as an important regulator of the Dsg1 genes in the context of hair anchorage and epidermal differentiation, and suggest that cadherin family genes are key targets of the grainy head-like genes across 700 million years of evolution.

Regional neural tube closure defined by the Grainy head-like transcription factors.

Primary neurulation in mammals has been defined by distinct anatomical closure sites, at the hindbrain/cervical spine (closure 1), forebrain/midbrain boundary (closure 2), and rostral end of the forebrain (closure 3). Zones of neurulation have also been characterized by morphologic differences in neural fold elevation, with non-neural ectoderm-induced formation of paired dorso-lateral hinge points (DLHP) essential for neural tube closure in the cranial and lower spinal cord regions, and notochord-induced bending at the median hinge point (MHP) sufficient for closure in the upper spinal region. Here we identify a unifying molecular basis for these observations based on the function of the non-neural ectoderm-specific Grainy head-like genes in mice. Using a gene-targeting approach we show that deletion of Grhl2 results in failed closure 3, with mutants exhibiting a split-face malformation and exencephaly, associated with failure of neuro-epithelial folding at the DLHP. Loss of Grhl3 alone defines a distinct lower spinal closure defect, also with defective DLHP formation. The two genes contribute equally to closure 2, where only Grhl gene dosage is limiting. Combined deletion of Grhl2 and Grhl3 induces severe rostral and caudal neural tube defects, but DLHP-independent closure 1 proceeds normally in the upper spinal region. These findings provide a molecular basis for non-neural ectoderm mediated formation of the DLHP that is critical for complete neuraxis closure.

Tgfbeta signaling directly induces Arf promoter remodeling by a mechanism involving Smads 2/3 and p38 MAPK.

We have investigated how the Arf gene product, p19(Arf), is activated by Tgfß during mouse embryo development to better understand how this important tumor suppressor is controlled. Taking advantage of new mouse models, we provide genetic evidence that Arf lies downstream of Tgfß signaling in cells arising from the Wnt1-expressing neural crest and that the anti-proliferative effects of Tgfß depend on Arf in vivo. Tgfß1, -2, and -3 (but not BMP-2, another member of the Tgfß superfamily) induce p19(Arf) expression in wild type mouse embryo fibroblasts (MEFs), and they enhance Arf promoter activity in Arf(lacZ/lacZ) MEFs. Application of chemical inhibitors of Smad-dependent and -independent pathways show that SB431542, a Tgfß type I receptor (TßrI) inhibitor, and SB203580, a p38 MAPK inhibitor, impede Tgfß2 induction of Arf. Genetic studies confirm the findings; transient knockdown of Smad2, Smad3, or p38 MAPK blunt Tgfß2 effects, as does Cre recombinase treatment of Tgfbr2(fl/fl) MEFs to delete Tgfß receptor II. Chromatin immunoprecipitation reveals that Tgfß rapidly induces Smads 2/3 binding and histone H3 acetylation at genomic DNA proximal to Arf exon 1ß. This is followed by increased RNA polymerase II binding and progressively increased Arf primary and mature transcripts from 24 through 72 h, indicating that increased transcription contributes to p19(Arf) increase. Last, Arf induction by oncogenic Ras depends on p38 MAPK but is independent of TßrI activation of Smad 2. These findings add to our understanding of how developmental and tumorigenic signals control Arf expression in vivo and in cultured MEFs.

Inositol- and folate-resistant neural tube defects in mice lacking the epithelial-specific factor Grhl-3.

The neural tube defects (NTDs) spina bifida and anencephaly are widely prevalent severe birth defects. The mouse mutant curly tail (ct/ct) has served as a model of NTDs for 50 years, even though the responsible genetic defect remained unrecognized. Here we show by gene targeting, mapping and genetic complementation studies that a mouse homolog of the Drosophila grainyhead (grh) gene, grainyhead-like-3 (Grhl3), is a compelling candidate for the gene underlying the curly tail phenotype. The NTDs in Grhl3-null mice are more severe than those in the curly tail strain, as the Grhl3 alleles in ct/ct mice are hypomorphic. Spina bifida in ct/ct mice is folate resistant, but its incidence can be markedly reduced by maternal inositol supplementation periconceptually. The NTDs in Grhl3-/- embryos are also folate resistant, but unlike those in ct/ct mice, they are resistant to inositol. These findings suggest that residual Grhl3 expression in ct/ct mice may be required for inositol rescue of folate-resistant NTDs.