Biology subjects

Banerjee, J.

Publications and source records attributed to Banerjee, J..

3 recordsLinked to original sources

bioRxiv2020

Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1

Neurofibromatosis type 1 is a monogenic syndrome that gives rise to numerous symptoms including cognitive impairment, skeletal abnormalities, and growth of benign nerve sheath tumors. Nearly all NF1 patients develop cutaneous neurofibromas (cNFs), which occur on the skin surface, while 40-60% of patients develop plexiform neurofibromas (pNFs) which are deeply embedded in the peripheral nerves. Patients with pNFs have a [~]10% lifetime chance of these tumors becoming malignant peripheral nerve sheath tumors (MPNSTs). These tumors have a severe prognosis and few treatment options other than surgery. Given the lack of therapeutic options available to patients with these tumors, identification of druggable pathways or other key molecular features could aid ongoing therapeutic discovery studies. In this work, we used statistical and machine learning methods to analyze 77 NF1 tumors with genomic data to characterize key signaling pathways that distinguish these tumors and identify candidates for drug development. We identified subsets of latent gene expression variables that may be important in the identification and etiology of cNFs, pNFs, other neurofibromas, and MPNSTs. Furthermore, we characterized the association between these latent variables and genetic variants, immune deconvolution predictions, and protein activity predictions.

systems biology↗

bioRxiv2019

A clinically and genomically annotated nerve sheath tumor biospecimen repository.

Nerve sheath tumors occur as a heterogeneous group of neoplasms in patients with neurofibromatosis type 1 (NF1). The malignant form represents the most common cause of death in people with NF1, and even when benign, these tumors can result in significant disfigurement, neurologic dysfunction, and a range of profound symptoms. Lack of human tissue across the peripheral nerve tumors common in NF1 has been a major limitation in the development of new therapies. To address this unmet need, we have created an annotated collection of patient tumor samples, patient-derived cell lines, and patient-derived xenografts, and carried out high-throughput genomic and transcriptomic characterization to serve as a resource for further biologic and preclinical therapeutic studies. In this work, we release genomic and transcriptomic datasets comprised of 55 tumor samples derived from 23 individuals, complete with clinical annotation. All data are publicly available through the NF Data Portal and at http://synapse.org/jhubiobank.

cancer biology↗

bioRxiv2019

Physico-biochemical and molecular responses of Acacia auriculiformis to salinity stress

Salinity limits the growth and yield of many crops across the globe and is considered as major threat to agriculture. Acacia auriculiformis, an important salt tolerant crop, is growing abundantly in the salt-affected mangrove areas of Sunderban, West Bengal, India. In the present study, we have reported the physiological, molecular and antioxidant response of this crop to a gradient of salt treatments ranging between 0 and 800 mM NaCl. As a stress response, the antioxidant enzymes viz. superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (GPX) were highly activated at 200, 400 and 800 mM NaCl respectively. Antioxidant metabolites such as phenols and thiols elevated with increasing salt treatments thus augmenting antioxidant activity with significant positive relationship with phenol content. Similarly, phenylalanine ammonia lyase (PAL) activity was up-regulated in a dose dependent manner with significant relationship with phenol content. This study also reported the phenolic profile for the first time in A. auriculiformis with the abundance of flavonoids. In addition, transcriptional up-regulation of Na+/H+ antiporter gene (NHX1) and the development of robust vascular tissues was noticed at 400 mM NaCl stress compared to control, while further stress at 800 mM NaCl induced poor vascular tissue growth but with higher PAL activity and consequent higher phenol content. Based on this observation, a model for salt tolerance mechanism of A. auriculiformis has been proposed.

biochemistry↗