Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. It manifests along multiple phenotypic axes and decoding the interconnections among these different axes is crucial to understand its molecular origins and to develop novel therapeutic strategies to control it. Here, we use multi-modal transcriptomic data analysis - bulk, single-cell and spatial transcriptomics - from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity - two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. These patterns were inherent in methylation profiles, suggesting an epigenetic crosstalk between EMT and lineage plasticity in breast cancer. Mathematical modelling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes recapitulate and thus elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and to identify possible interventions to restrict it.

FKBP14 kyphoscoliotic Ehlers-Danlos syndrome misdiagnosed as Larsen syndrome: a case report.

Hereditary connective tissue disorders have overlapping phenotypes, particularly in regard to musculoskeletal features. This contributes to the challenge of phenotype-based clinical diagnoses. However, some hereditary connective tissue disorders have distinct cardiovascular manifestations that require early intervention and specific management. Molecular testing has increased the ability to categorize and diagnose distinct hereditary connective tissue disorders. A 42-yr-old female with a clinical diagnosis of Larsen syndrome from birth presented for genetic testing based on her recent diagnosis of premenopausal breast cancer. She had a past medical history of multiple carotid dissections. As she never had confirmatory molecular genetic testing for Larsen syndrome, whole-exome sequencing was utilized to assess both hereditary cancer predisposition syndromes and connective tissue disorders. A homozygous pathogenic variant in the FKBP14 gene was identified associated with FKBP14 kyphoscoliotic Ehlers-Danlos syndrome. We recommend that patients with a clinical diagnosis of Larsen syndrome undergo broad-based molecular sequencing for multiple hereditary connective tissue disorders. Molecular diagnosis is particularly crucial for all individuals who have a history of significant vascular events in the setting of a clinical diagnosis only. Early diagnosis of a hereditary connective tissue disorder with vascular features allows for screening and subsequent prevention of cardiovascular events.

Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis.

The SARS-CoV-2 is one of the most infectious and deadly coronaviruses, which has gripped the world, causing the COVID-19 pandemic. Despite the numerous studies being conducted on this virus, many uncertainties are with the disease. This is exacerbated by the speedy mutations acquired by the viral strain, which enables the disease to present itself differently in different people, introducing new factors of uncertainty. This study aims at the identification of regulatory pathways across two cell lines, namely, the peripheral blood mononuclear cell line (PBMC) and the normal human bronchial epithelial (NHBE) cell line. Both the above-mentioned cell lines were considered because they support viral replication. Furthermore, the NHBE cell line captures vital changes in the lungs, which are the main organs affected by the COVID-19 patients, and the PBMC cell line is closely linked to the body's immune system. RNA-Seq analysis, differential gene expression and gene set enrichment analysis for pathway identification were followed. Pathway analysis throws light upon the various systems affected in the body due to the COVID-19. Gene regulatory networks associated with the significant pathways were also designed. These networks aid in identifying various gene targets, along with their interactions. Studying the functionality of the pathways and the gene interactions associated with them, aided by long COVID studies, will provide immense clarity about the current COVID-19 scenario. In the long term, this will help in the design of therapeutic approaches against the SARS-CoV-2 and can also contribute to drug repurposing studies. Ultimately, this study identifies and analyses the relationship of various undiscovered or lesser explored pathways in the human body to the SARS-CoV-2 and establish a clearer picture of the association to help streamline further studies and approaches.

A call for unity in DEIJ efforts using a proposed framework for Education, Recruitment, Retainment, Research, and Active outreach (ERA) for genetic counselors in the United States.

Genetic counselors, like many other healthcare providers, play a vital role in genomic health care. As a profession, we, along with our colleagues and students, have recognized the need to improve and incorporate diversity, equity, inclusion, and justice (DEIJ) within our daily ways of practice to help create access to genomic technologies. In order to create systemic change and focus on unity, open communication, and transparency, we introduce a suggested framework called ERA (Education, Recruitment, Retainment, Research, and Active Outreach). This framework would benefit a genetic counselor throughout various stages of their career, from student to practicing genetic counselor, and can be broadly applied to all specialties of genomic medicine. Different iterations of DEIJ efforts have arisen in the National Society of Genetic Counselors (NSGC), from the D&I (Diversity and Inclusion) Task Force to the J.E.D.I (justice, equity, diversity, and inclusion) committee. The lack of recorded history of these previous efforts and the lack of communication between current DEIJ organizations is one of the many reasons the ERA framework demands unity and transparency to achieve sustainable positive change. Genetic counselors must unite and work collaboratively to conduct and promote DEIJ efforts, so the benefits of genomic medicine can be realized by all.

Dyrk1b promotes hepatic lipogenesis by bypassing canonical insulin signaling and directly activating mTORC2 in mice.

Mutations in Dyrk1b are associated with metabolic syndrome and nonalcoholic fatty liver disease in humans. Our investigations showed that DYRK1B levels are increased in the liver of patients with nonalcoholic steatohepatitis (NASH) and in mice fed with a high-fat, high-sucrose diet. Increasing Dyrk1b levels in the mouse liver enhanced de novo lipogenesis (DNL), fatty acid uptake, and triacylglycerol secretion and caused NASH and hyperlipidemia. Conversely, knockdown of Dyrk1b was protective against high-calorie-induced hepatic steatosis and fibrosis and hyperlipidemia. Mechanistically, Dyrk1b increased DNL by activating mTORC2 in a kinase-independent fashion. Accordingly, the Dyrk1b-induced NASH was fully rescued when mTORC2 was genetically disrupted. The elevated DNL was associated with increased plasma membrane sn-1,2-diacylglyerol levels and increased PKCε-mediated IRKT1150 phosphorylation, which resulted in impaired activation of hepatic insulin signaling and reduced hepatic glycogen storage. These findings provide insights into the mechanisms that underlie Dyrk1b-induced hepatic lipogenesis and hepatic insulin resistance and identify Dyrk1b as a therapeutic target for NASH and insulin resistance in the liver.

Epistatic interaction of PDE4DIP and DES mutations in familial atrial fibrillation with slow conduction.

The genetic causes of atrial fibrillation (AF) with slow conduction are unknown. Eight kindreds with familial AF and slow conduction, including a family affected by early-onset AF, heart block, and incompletely penetrant nonischemic dilated cardiomyopathy (DCM) underwent whole exome sequencing. A known pathogenic mutation in the desmin (DES) gene resulting in p.S13F substitution (NM_001927.3:c.38C>T) at a PKC phosphorylation site was identified in all four members of the kindred with early-onset AF and heart block, while only two developed DCM. Higher penetrance for AF and heart block prompted a genetic screening for DES modifier(s). A deleterious mutation in the phosphodiesterase-4D-interacting-protein (PDE4DIP) gene resulting in p.A123T substitution (NM_001002811:c.367G>A) was identified that segregated with early-onset AF, heart block, and the DES mutation. Three additional novel deleterious PDE4DIP mutations were identified in four other unrelated kindreds. Characterization of PDE4DIPA123T in vitro suggested impaired compartmentalization of PKA and PDE4D characterized by reduced colocalization with PDE4D, increased cAMP activation leading to higher PKA phosphorylation of the ß2-adrenergic-receptor, and decreased PKA phosphorylation of desmin after isoproterenol stimulation. Our findings identify PDE4DIP as a novel gene for slow AF and unravel its epistatic interaction with DES mutations in development of conduction disease and arrhythmia.

The role of Wnt signalling in development of coronary artery disease and its risk factors.

The Wnt signalling pathways are composed of a highly conserved cascade of events that govern cell differentiation, apoptosis and cell orientation. Three major and distinct Wnt signalling pathways have been characterized: the canonical Wnt pathway (or Wnt/ß-catenin pathway), the non-canonical planar cell polarity pathway and the non-canonical Wnt/Ca2+ pathway. Altered Wnt signalling pathway has been associated with diverse diseases such as disorders of bone density, different malignancies, cardiac malformations and heart failure. Coronary artery disease is the most common type of heart disease in the United States. Atherosclerosis is a multi-step pathological process, which starts with lipid deposition and endothelial cell dysfunction, triggering inflammatory reactions, followed by recruitment and aggregation of monocytes. Subsequently, monocytes differentiate into tissue-resident macrophages and transform into foam cells by the uptake of modified low-density lipoprotein. Meanwhile, further accumulations of lipids, infiltration and proliferation of vascular smooth muscle cells, and deposition of the extracellular matrix occur under the intima. An atheromatous plaque or hyperplasia of the intima and media is eventually formed, resulting in luminal narrowing and reduced blood flow to the myocardium, leading to chest pain, angina and even myocardial infarction. The Wnt pathway participates in all different stages of this process, from endothelial dysfunction to lipid deposit, and from initial inflammation to plaque formation. Here, we focus on the role of Wnt cascade in pathophysiological mechanisms that take part in coronary artery disease from both clinical and experimental perspectives.

Genetic counseling education at the undergraduate level: An outreach initiative to promote professional recruitment and support workforce development.

As in many other countries, the field of genetic counseling is in its initial stages of development in India, where there are efforts to streamline the profession and to implement graduate-level training programs. We implemented an elective course on genetic counseling at the undergraduate level in a private university in India to assess students' interest, to provide early exposure for students interested in pursuing the career, and to aid recruitment. To assess satisfaction with the course and recruitment outcomes, we sent a course evaluation survey to 332 students and received 134 responses. Familiarity with genetic counseling topics increased significantly after completing the course. Of the 42 respondents who reported they were planning to pursue formal genetic counseling training, 21% (n = 9/42) became interested in the profession as a result of taking this course. Survey respondents who were prospective applicants to genetic counseling training programs referred mostly to the websites of the National Society of Genetic Counselors and the American Board of Genetic Counseling for information on genetic counseling and training. Barriers to entry into the field included lack of shadowing opportunities, inadequate coursework, and limited opportunities to interact with practicing genetic counselors. Respondents stated that additional case studies as well as observation of patient interactions would elucidate the role of a genetic counselor and help define the scope of the practice in India and other countries. Overall, genetic counseling education at the undergraduate level is a scalable way to improve understanding of genetic counseling topics, increase professional interest in the field, and support workforce development.

Palladium-mediated intramolecular aryl amination on furanose derivatives: an expedient approach to the synthesis of chiral benzoxazocine derivatives and tricyclic nucleosides.

Pd-catalyzed intramolecular arylamination on sugar derivatives has been accomplished by using bulky biaryl phosphine ligands. An application of this methodology on a variety of D-glucose-derived substrates, 2a-f, led to the synthesis of highly functionalized cis-fused tricyclic oxazocines, 3a-e. The products could subsequently be transformed to the optically active benzoxazocine derivative 4 and tricyclic nucleoside 6. This is the first example of the synthesis of eight-membered rings via intramolecular cycloamination of furanose derivatives, which provides a very useful method for the catalytic synthesis of medium-ring heterocycles.