Comparative transcriptome analyses reveal insights into catkin bloom patterns in pecan protogynous and protandrous cultivars.

In perennial plants such as pecan, once reproductive maturity is attained, there are genetic switches that are regulated and required for flower development year after year. Pecan trees are heterodichogamous with both pistillate and staminate flowers produced on the same tree. Therefore, defining genes exclusively responsible for pistillate inflorescence and staminate inflorescence (catkin) initiation is challenging at best. To understand these genetic switches and their timing, this study analyzed catkin bloom and gene expression of lateral buds collected from a protogynous (Wichita) and a protandrous (Western) pecan cultivar in summer, autumn and spring. Our data showed that pistillate flowers in the current season on the same shoot negatively impacted catkin production on the protogynous 'Wichita' cultivar. Whereas fruit production the previous year on 'Wichita' had a positive effect on catkin production on the same shoot the following year. However, fruiting the previous year nor current year pistillate flower production had no significant effect on catkin production on 'Western' (protandrous cultivar) cultivar. The RNA-Seq results present more significant differences between the fruiting and non-fruiting shoots of the 'Wichita' cultivar compared to the 'Western' cultivar, revealing the genetic signals likely responsible for catkin production. Our data presented here, indicates the genes showing expression for the initiation of both types of flowers the season before bloom.

Overcoming biases in causal inference of molecular interactions.

MOTIVATION: Computer inference of biological mechanisms is increasingly approachable due to dynamically rich data sources such as single-cell genomics. Inferred molecular interactions can prioritize hypotheses for wet-lab experiments to expedite biological discovery. However, complex data often come with unwanted biological or technical variations, exposing biases over marginal distribution and sample size in current methods to favor spurious causal relationships. RESULTS: Considering function direction and strength as evidence for causality, we present an adapted functional chi-squared test (AdpFunChisq) that rewards functional patterns over non-functional or independent patterns. On synthetic and three biology datasets, we demonstrate the advantages of AdpFunChisq over 10 methods on overcoming biases that give rise to wide fluctuations in the performance of alternative approaches. On single-cell multiomics data of multiple phenotype acute leukemia, we found that the T-cell surface glycoprotein CD3 delta chain may causally mediate specific genes in the viral carcinogenesis pathway. Using the causality-by-functionality principle, AdpFunChisq offers a viable option for robust causal inference in dynamical systems. AVAILABILITY AND IMPLEMENTATION: The AdpFunChisq test is implemented in the R package 'FunChisq' (2.5.2 or above) at https://cran.r-project.org/package=FunChisq. All other source code along with pre-processed data is available at Code Ocean https://doi.org/10.24433/CO.2907738.v1. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

Detecting genetic epistasis by differential departure from independence.

Countering prior beliefs that epistasis is rare, genomics advancements suggest the other way. Current practice often filters out genomic loci with low variant counts before detecting epistasis. We argue that this practice is far from optimal because it can throw away strong epistatic patterns. Instead, we present the compensated Sharma-Song test to infer genetic epistasis in genome-wide association studies by differential departure from independence. The test does not require a minimum number of replicates for each variant. We also introduce algorithms to simulate epistatic patterns that differentially depart from independence. Using two simulators, the test performed comparably to the original Sharma-Song test when variant frequencies at a locus are marginally uniform; encouragingly, it has a marked advantage over alternatives when variant frequencies are marginally nonuniform. The test further revealed uniquely clean epistatic variants associated with chicken abdominal fat content that are not prioritized by other methods. Genes involved in most numbers of inferred epistasis between single nucleotide polymorphisms (SNPs) belong to pathways known for obesity regulation; many top SNPs are located on chromosome 20 and in intergenic regions. Measuring differential departure from independence, the compensated Sharma-Song test offers a practical choice for studying epistasis robust to nonuniform genetic variant frequencies.

Fundamental gene network rewiring at the second order within and across mammalian systems.

MOTIVATION: Genetic or epigenetic events can rewire molecular networks to induce extraordinary phenotypical divergences. Among the many network rewiring approaches, no model-free statistical methods can differentiate gene-gene pattern changes not attributed to marginal changes. This may obscure fundamental rewiring from superficial changes. RESULTS: Here we introduce a model-free Sharma-Song test to determine if patterns differ in the second order, meaning that the deviation of the joint distribution from the product of marginal distributions is unequal across conditions. We prove an asymptotic chi-squared null distribution for the test statistic. Simulation studies demonstrate its advantage over alternative methods in detecting second-order differential patterns. Applying the test on three independent mammalian developmental transcriptome datasets, we report a lower frequency of co-expression network rewiring between human and mouse for the same tissue group than the frequency of rewiring between tissue groups within the same species. We also find second-order differential patterns between microRNA promoters and genes contrasting cerebellum and liver development in mice. These patterns are enriched in the spliceosome pathway regulating tissue specificity. Complementary to previous mammalian comparative studies mostly driven by first-order effects, our findings contribute an understanding of system-wide second-order gene network rewiring within and across mammalian systems. Second-order differential patterns constitute evidence for fundamentally rewired biological circuitry due to evolution, environment or disease. AVAILABILITY AND IMPLEMENTATION: The generic Sharma-Song test is available from the R package 'DiffXTables' at https://cran.r-project.org/package=DiffXTables. Other code and data are described in Section 2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Intraglomerular micrometastasis of squamous cell carcinoma.

Intraglomerular metastasis is a rare manifestation of disseminated malignancies. We present here a case of intraglomerular metastatic carcinoma diagnosed as an incidental finding on a kidney biopsy in a 62-year-old male presenting with acute renal failure and metastatic penile squamous cell carcinoma. A proliferative lesion composed of highly atypical epithelial cells was found within a capillary loop and adjacent urinary space of an isolated glomerulus, which was immunoreactive for markers of squamous cell carcinoma. This case is a reminder that circulating cancer cells can occasionally lodge in glomeruli and appear as micrometastasis in kidney biopsies performed for the evaluation of renal dysfunction.

Hepatitis B vaccination in human immunodeficiency virus-infected adults receiving hemodialysis.

BACKGROUND: The Centers for Disease Control and Prevention (CDC) recommends hepatitis B virus (HBV) immunization for all hemodialysis (HD) patients because they are at high risk of infection. Several studies have shown that the development of protective antibody titers after HBV vaccination is much lower in HD patients. We hypothesized that human immunodeficiency virus (HIV) infection in patients with end-stage renal disease (ESRD) would further impair the immune response to hepatitis B vaccination. METHODS: We performed a retrospective cohort study of patients undergoing long-term hemodialysis from 1990 to 2002 at the United States-based dialysis facilities of Gambro Corporation, North America. The response rate defined as an increase in anti-HBs levels >/=10 mIU/L after a month of the third dose of HBV vaccination was determined in HIV-infected and a randomly selected group of ESRD patients. The demographic information, laboratory data, and hepatitis B surface antibody (anti-HBs) titers were recorded from the Gambro Corporation database on these patients. RESULTS: Of the 347 adult HIV ESRD patients, 116 received three doses of recombinant hepatitis B vaccination. Seventy percent were male, and the majority (86%) were black. Of the 116 patients who received three doses of HBV vaccination, 62 (53.4%) developed protective antibody titers. This was comparable to the response rate of 50.4% in the randomly selected 220 non-HIV hemodialysis patients. Among HIV ESRD patients, the mean hemoglobin (Hgb) was higher in patients who developed protective antibody titers (Hgb 11.61 +/- 2 vs. 10.55 +/- 1.86, P value <0.01). On multivariate logistic regression analysis, higher Hgb was associated with protective antibody titers (odds ratio: 1.34, 95% CI 0.99-1.72). Seventy percent of the HIV-infected responders maintained protective antibody titers 6 months after vaccination. CONCLUSION: Hepatitis B vaccination should be offered to all HIV-infected ESRD patients because over half of the patients with HIV and ESRD can develop protective antibodies.