Abstract 1459: Identification of transcription factor enrichments in HPV+ head and neck cancer using ChIP-seq and cistrome analysis

The subset of head and neck squamous cell carcinomas (HNSCC) that are driven by infection with the Human Papilloma Virus (HPV+ HNSCC) are increasing in prevalence and are defined by distinct biological signatures and mechanisms, such as abnormal transcriptional regulation. Here, we use optimized protocols to perform ChIP-seq and RNA-seq on patient surgical samples, which we use to define promoter, typical-enhancer, and super-enhancer (SE) regulatory regions with differential chromatin states (i.e. H3K27ac signal) between tumor and normal samples. We then leverage publicly available transcription factor (TF) cistrome data to test 372 TFs for tumor or normal specific enrichment across these differential regulatory regions. We identify 31 tumor-specific TF enrichments, such as TP53/63/73, NKX2-1, JUNB/D, FOSL1/2, E2F1/3, KLF3/4/5, SMAD3/4, TEAD1/4, TFAP2A/C, HIF1A, PPARG, GRHL2, EPAS1, and SNAI2. A number of these enriched TFs, including TP63, TP73, FOSL1, and E2F1, show both significantly increased expression in tumors and significant transcriptional reductions after JQ1 treatment. These results provide novel insight into the regulatory biology of HPV+ HNSCC, and suggest that the transcriptional networks and feedback loops governing TF expression and dysregulation in HPV+ HNSCC can be targeted using JQ1 treatment.

Citation Format: Fernando Zamuner, Spencer S. Chan, Michael Kessler, Ilya Vorontsov, Ludmila Danilova, Rossin Erbe, Dylan Kelley, Theresa Guo, Eddie Imada, Elana J. Fertig, Ivan Kulakovskiy, Alexander Favorov, Daria A. Gaykalova. Identification of transcription factor enrichments in HPV+ head and neck cancer using ChIP-seq and cistrome analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1459.

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

BACKGROUND

Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological applications. This calls for comprehensive benchmarking of public PWM models with large experimental reference sets.

RESULTS

Here we report results from all-against-all benchmarking of PWM models for DNA binding sites of human TFs on a large compilation of in vitro (HT-SELEX, PBM) and in vivo (ChIP-seq) binding data. We observe that the best performing PWM for a given TF often belongs to another TF, usually from the same family. Occasionally, binding specificity is correlated with the structural class of the DNA binding domain, indicated by good cross-family performance measures. Benchmarking-based selection of family-representative motifs is more effective than motif clustering-based approaches. Overall, there is good agreement between in vitro and in vivo performance measures. However, for some in vivo experiments, the best performing PWM is assigned to an unrelated TF, indicating a binding mode involving protein-protein cooperativity.

CONCLUSIONS

In an all-against-all setting, we compute more than 18 million performance measure values for different PWM-experiment combinations and offer these results as a public resource to the research community. The benchmarking protocols are provided via a web interface and as docker images. The methods and results from this study may help others make better use of public TF specificity models, as well as public TF binding data sets.

Abstract 5206: Role of super-enhancers in HPV+ head and neck squamous cell carcinoma

Head and neck squamous cell carcinomas (HNSCC) are the sixth leading cause of cancer worldwide with different incidences, mortalities, and prognosis for different subsites. Infection by Human Papilloma Viral (HPV) can cause the development of HPV+ HNSCC, the most rapidly growing population of cancer patients. The molecular biology of HPV+ HNSCC is related to abnormal transcriptional regulation. Super-enhancers (SEs) were recently identified as critical regulators of gene expression during cell differentiation and disease development. SEs are long clusters of enhancers that recruit master transcription factors (TFs) and coactivators to regulate the expression of target genes. We have recently developed a new whole-genome analytical pipeline to optimize ChIP-Seq procedures on primary surgical samples, and this protocol helped us to define the whole-genome distribution of H3K27ac, the hallmark of SEs, in HPV+ HNSCC samples. To detect SEs, we used a novel LILY algorithm that corrects the ChIP-Seq signal for copy number variation and CpG density. The analysis revealed that HPV+ HNSCC-specific SEs regulate genes critical for head and neck cancer development, such as EGFR, TP63, JAG1, IRF6, SMAD3, MAP4K2, SNAI1, TNFAIP3, ANO2, and TNFRSF1A. These genes are located in the vicinity of HNSCC-specific SEs, and the expression of those genes was altered by JQ1, the inhibitor of BRD4, the main component of SE machinery, supporting the role of SE in their regulation. The following Cistrome analysis allowed us to elucidate the TF composition of the SE machinery. Thus, we have found out that P63, P53, SOX2, FOSL1, SMAD3, and SNAI2 are TFs that are the most overrepresented in the HPV+ HNSCC-specific SEs. These comprehensive analyses have revealed novel insight into the HPV+ HNSCC biology and paved the basis for the implications for epigenetic therapeutics for this tumor types, and potentially other virus-related malignancies.

Citation Format: Fernando T. Zamuner, Ilya Vorontsov, Emily Flam, Vera Mukhina, Ludmila Danilova, Tingting Ou, Elena Stavrovskaya, Theresa Guo, Eric Windsor, Dylan Z. Kelley, Michael Parfenov, Michael Considine, Elana J. Fertig, Alexander Favorov, Daria A. Gaykalova. Role of super-enhancers in HPV+ head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5206.

In silico motif analysis suggests an interplay of transcriptional and translational control in mTOR response

The short 5'-terminal oligopyrimidine tract (TOP) of 5' UTRs is a well-known regulatory sequence motif of mRNAs that are subject to growth-dependent translation. Specifically, translation of TOP mRNAs is regulated by the mTOR signaling pathway that is involved in cell proliferation, cancer development and aging. High throughput data permit detailed study of specific features of the mRNA TOP motif and its DNA origins at transcription start sites (TSS). Recently, ribosome profiling was used to identify mRNA targets of the mTOR pathway in PC3 cells. A novel pyrimidine-rich translational element (PRTE) was reported to play a key role without positional preferences within the 5' UTRs, unlike 5' TOP, which are strictly located at the 5' ends. In this study, we couple recently reported ribosome profiling data on the mTOR mRNA targets with the annotation of TSS obtained by HeliScopeCAGE. We confirm the canonical TOP and strong positional preferences of respective oligopyrimidine tracts (OP) straddling the experimentally validated TSS regions at the DNA level. Such OP localization ensures that transcription from OP segments creates the 5'-terminal TOP in the corresponding mRNAs. We demonstrate that OP are not overrepresented in downstream regions of 5' UTRs of mTOR targets. Finally, we highlight several mTOR target genes with broad and multimodal TSS spanning dozens of nucleotides that are only partically covered with an OP. Therefore, in such cases only a fraction of all produced mRNAs carry a TOP regulatory motif and, thus, respond to mTOR via TOP mechanism. We hypothesize that the interplay between transcription and translation may play a crucial role in the regulation of the mTOR response.

From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) became a method of choice to locate DNA segments bound by different regulatory proteins. ChIP-Seq produces extremely valuable information to study transcriptional regulation. The wet-lab workflow is often supported by downstream computational analysis including construction of models of nucleotide sequences of transcription factor binding sites in DNA, which can be used to detect binding sites in ChIP-Seq data at a single base pair resolution. The most popular TFBS model is represented by positional weight matrix (PWM) with statistically independent positional weights of nucleotides in different columns; such PWMs are constructed from a gapless multiple local alignment of sequences containing experimentally identified TFBSs. Modern high-throughput techniques, including ChIP-Seq, provide enough data for careful training of advanced models containing more parameters than PWM. Yet, many suggested multiparametric models often provide only incremental improvement of TFBS recognition quality comparing to traditional PWMs trained on ChIP-Seq data. We present a novel computational tool, diChIPMunk, that constructs TFBS models as optimal dinucleotide PWMs, thus accounting for correlations between nucleotides neighboring in input sequences. diChIPMunk utilizes many advantages of ChIPMunk, its ancestor algorithm, accounting for ChIP-Seq base coverage profiles ("peak shape") and using the effective subsampling-based core procedure which allows processing of large datasets. We demonstrate that diPWMs constructed by diChIPMunk outperform traditional PWMs constructed by ChIPMunk from the same ChIP-Seq data. Software website: http://autosome.ru/dichipmunk/

The effect of Russian Maternity Home routines on breastfeeding and neonatal weight loss with special reference to swaddling

BACKGROUND

Few investigations have considered evaluating the effects of certain combinations of ward routines like swaddling of the baby and separation of mother and baby on infant variables such as neonatal weight loss.

AIMS

To study the effect of different ward routines in respect to proximity to mother and type of infant apparel, on breastfeeding parameters (amount of ingested milk, volume of supplements, number of breastfeeds, total duration of breastfeeding time) day 4 after birth as well as recovery from neonatal weight loss and infant's weight on day 5.

STUDY DESIGN AND SUBJECTS

In a randomized trial with factorial design four treatment groups including 176 mother-infant dyads were studied 25-120 min after birth. Randomized treatments focused on care routines administered to the infants after delivery and later in the maternity ward as well as to the type of clothing the infants received. Group 1 infants were placed skin-to-skin with their mothers after delivery, and had rooming-in while in the maternity ward. Group 2 infants were dressed and placed in their mothers' arms after delivery, and roomed-in with mothers in the maternity ward. Group 3 infants were kept in the nursery both after birth and while their mothers were in the maternity ward. Group 4 infants were kept in the nursery after birth, but roomed-in with their mothers in the maternity ward. Equal numbers of infants were either swaddled or clothed in baby attire. Breastfeeding parameters were documented during day 4 after birth. Infant's weight was measured daily.

RESULTS

Babies who were kept in the nursery received significantly more formula and significantly less breast-milk, than did babies who roomed-in with their mothers. Swaddling did not influence the breastfeeding parameters measured. However, swaddled babies who had experienced a 2-h separation period after birth and then were reunited with their mothers tended to have a delayed recovery of weight loss compared to those infants who were exposed to the same treatment but dressed in clothes. Furthermore, swaddled babies who were kept in the nursery and received breast-milk supplements had a significantly delayed recovery of weight loss after birth when compared to those infants ingesting only breast-milk. On day 5, regression analyses of predicted weight gain in the exclusively breastfed infants indicated a significant increase per 100 ml breast-milk (59 g), compared to the predicted weight gain on day 5 per 100 ml supplements in the swaddled babies (14 g) (P=0.001).

CONCLUSION

Supplements given to the infants in the nursery had a negative influence on the amount of milk ingested. In addition, supplement feeding or a short separation after birth when combined with swaddling was shown to have a negative consequence to infant weight gain.

Skin-to-skin contact may reduce negative consequences of "the stress of being born": a study on temperature in newborn infants, subjected to different ward routines in St. Petersburg

AIM

To evaluate how different delivery-ward routines influence temperature in newborn infants.

METHODS

A total of 176 newborn mother-infant pairs were included in a randomized study. The babies were kept skin-to-skin on the mother's chest (Skin-to-skin group), held in their mother's arms, being either swaddled or clothed (Mother's arms group), or kept in a cot in the nursery, being either swaddled or clothed (Nursery group). Temperature was measured in the axilla, on the thigh, back and foot at 15-min intervals at from 30 to 120 min after birth.

RESULTS

During this time period the axilla, back and thigh temperatures rose significantly in all the treatment groups. The foot temperature displayed a significant fall in the babies in the Nursery group and this decrease was greatest in the swaddled babies. In contrast, foot temperature rose in the babies in the Mother's arms group and in particular in babies in the Skin-to-skin group. Foot temperature remained high in the Skin-to-skin group, whereas the low temperature observed in the Nursery group gradually increased and two days after birth the difference was no longer significant.

CONCLUSION

The results show that delivery-ward routines influence skin temperature in infants in the postnatal period. Allowing mother and baby the ward routine of skin-to-skin contact after birth may be a "natural way" of reversing stress-related effects on circulation induced during labour.

Methotrexate in resistant juvenile rheumatoid arthritis. Results of the U.S.A.-U.S.S.R. double-blind, placebo-controlled trial. The Pediatric Rheumatology Collaborative Study Group and The Cooperative Children's Study Group

BACKGROUND

The antimetabolite methotrexate has been shown in placebo-controlled trials to be effective in adults with rheumatoid arthritis. Methotrexate may also be effective in children with resistant juvenile rheumatoid arthritis, but the supporting data are from uncontrolled trials.

METHODS

Centers in the United States and the Soviet Union participated in this randomized, controlled, double-blind trial designed to evaluate the effectiveness and safety of orally administered methotrexate. Patients received one of the following treatments each week for six months: 10 mg of methotrexate per square meter of body-surface area (low dose), 5 mg of methotrexate per square meter (very low dose), or placebo. The use of prednisone (less than or equal to 10 mg per day) and two nonsteroidal antiinflammatory drugs was also allowed.

RESULTS

The 127 children (mean age, 10.1 years) had a mean duration of disease of 5.1 years; 114 qualified for the analysis of efficacy. According to a composite index of several response variables, 63 percent of the children who received low-dose methotrexate improved, as compared with 32 percent of those in the very-low-dose group and 36 percent of those in the placebo group (P = 0.013). As compared with the placebo group, the low-dose group also had significantly larger mean reductions from base line in the number of joints with pain on motion (-11.0 vs. -7.1), the pain-severity score (-19 vs. -11.5), the number of joints with limited motion (-5.4 vs. -0.7), and the erythrocyte sedimentation rate (-19.0 vs. -6 mm per hour). In the methotrexate groups only three children had the drug discontinued because of mild-to-moderate side effects; none had severe toxicity.

CONCLUSIONS

Methotrexate given weekly in low doses is an effective treatment for children with resistant juvenile rheumatoid arthritis, and at least in the short term this regimen is safe.