Rimpi Khurana

• Doctor of Medicine
• Research Associate at University of Miami

Purpose: PTEN loss-of-function occurs in ~50% of metastatic, castrate-resistant prostate cancer (mCRPC) patients, and associated with poor prognosis and responsiveness to standard-of-care therapies and immune checkpoint inhibitors. While PTEN loss-of-function hyperactivates PI3K signaling, combinatorial PI3K/AKT pathway and androgen deprivation th...

Translocation t(11;14) positive multiple myeloma (MM) is sensitive to venetoclax, yet the drug lacks FDA approval in MM. Selinexor is an inhibitor of nuclear exporter XPO1 and is approved in relapsed refractory MM. We recently analyzed RNA-seq from 859 MM patient samples (MMRF CoMMpass study) and compared them to healthy bone marrow samples (GSE114...

PTEN loss-of-function occurs in approximately 50% of mCRPC patients, and is associated with a poor prognosis, therapeutic outcomes and resistance to immune-checkpoint inhibitors. Recent clinical studies demonstrated that dual PI3K/AKT pathway inhibition and androgen axis blockade led to a modest improvement in progression-free survival of PTEN-defi...

Kinases are among the most established druggable proteins with currently over 50 approved kinase inhibitor drugs, most of them for cancer. However, these drugs only target a small subset of the human kinome and many kinases remain “dark” or “understudied” (Essegian et al. 2020, Oprea et al. 2018 [1], [2]). To improve the utility to evaluate the cli...

Gastric cancer (GC) is frequently characterized by resistance to standard chemotherapeutic regimens and poor clinical outcomes. We aimed to identify a novel therapeutic approach using drug sensitivity testing (DST) and our computational SynerySeq pipeline. DST of GC cell lines was performed with a library of 215 Federal Drug Administration (FDA) ap...

The approval of the first kinase inhibitor, Gleevec, ushered in a paradigm shift for oncological treatment—the use of genomic data for targeted, efficacious therapies. Since then, over 48 additional small-molecule kinase inhibitors have been approved, solidifying the case for kinases as a highly druggable and attractive target class. Despite the ro...

The approval of the first kinase inhibitor, Gleevec, in 2001, ushered in a paradigm shift for oncological treatment; the use of genomic data for targeted, efficacious therapies. Since then, over 48 additional small molecule kinase inhibitors have been approved, solidifying the case for kinases as a highly druggable and attractive target class. Desp...

Kinases are firmly established drug targets in cancer. There are currently 44 FDA approved kinase drug and hundreds of compounds are in clinical development. However, less than 10% of the Kinome is currently targeted and a large proportion is considered understudied by the NIH Illuminating the Druggable Genome Program (https://druggablegenome.net/)...

Kinases are firmly established drug targets in cancer. There are currently 44 FDA approved kinase drug and hundreds of compounds are in clinical development. However, less than 10% of the Kinome is currently targeted and a large proportion is considered understudied by the NIH Illuminating the Druggable Genome Program (https://druggablegenome.net/)...

Background In melanoma, like in other cancers, both genetic alterations and epigenetic underlie the metastatic process. These effects are usually measured by changes in both methylome and transcriptome profiles, whose cross-correlation remains uncertain. We aimed to assess at systems scale the significance of epigenetic treatment in melanoma cells...

Biotype annotation. (XLSX)

DiP bio-annotations SKMEL-2. (XLSX)

lncRNA (lincRNome) cross-referencing. (PDF)

DEG profiles and ncRNA biotypes. (XLSX)

Cross-profiles (links between differential expression and differential methylation values). (XLSX)

DiP bio-annotations HS294T. (XLSX)

Measurements of methylation levels. (XLSX)

Biological validation. (RTF)

Biotype classification. (XLSX)

Implementation of gls function in R. (DOCX)

Chromatin (DAnCER) cross-referencing. (PDF)

In chronic kidney disease (CKD), the decline in glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has extensively been studied, little is known about the role of urinary exosomes and the...

Multiple system atrophy (MSA) is a fatal rapidly progressive α-synucleinopathy, characterized by α-synuclein accumulation in oligodendrocytes. It is accepted that the pathological α-synuclein accumulation in the brain of MSA patients plays a leading role in the disease process, but little is known about the events in the early stages of the disease...

(A) Overview of the experimental set-up. (B) Overlap of differentially expressed mRNAs resulting from microarray and RNA-seq analysis in SN. (C) To provide verification of the expression analysis defined by the two different methods we performed correlation analysis as demonstrated in a bladaltmanplot of the differences plotted against the averages...

Up-regulated miRNAs (right) and down-regulated miRNAs (left) in SN of MSA mice with the number of their predicted deregulated targets (expressed by blue color gradient). Predicted targets were assigned to enriched GO-terms (indicated at the bottom). (JPG)

Real-time PCR validation of the data for representative mRNA-miRNA predicted pairs in the striatum. (JPG)

List of differentially expressed mRNAs in the SN of MSA mice in a pre-motor stage of the disease. (XLSX)

List of differentially expressed miRNAs in the SN of MSA mice in a pre-motor stage of the disease. (XLSX)

List of miRNAs containing information about their predicted target genes and correlation values. This list was filtered for miRNA-target interactions, which (i) were predicted by mirWalk 2.0 with a p-value < 0.1, or (ii) were predicted by at least two prediction programs, or (iii) feature a validated target gene. In all cases, a minimum correlation...

List of enriched GO terms linked to differentially expressed mRNAs in the striatum of MSA mice in a pre-motor stage of the disease. (XLSX)

List of enriched GO terms linked to differentially expressed mRNAs in the SN of MSA mice in a pre-motor stage of the disease. (XLSX)

Clusters of GO biological processes and corresponding deregulated mRNAs in substantia nigra relevant to human MSA defined by REVIGO analysis. (XLSX)

Up-regulated miRNAs (right) and down-regulated miRNAs (left) in striatum of MSA mice with the number of their predicted deregulated targets (expressed by blue color gradient). Predicted targets were assigned to enriched GO-terms. (JPG)

List of primers used for RT-PCR analysis. (DOCX)

List of differentially expressed mRNAs in the striatum of MSA mice in a pre-motor stage of the disease. (XLSX)

List of differentially expressed miRNAs in the striatum of MSA mice in a pre-motor stage of the disease. (XLSX)

Real-time PCR verification of RNA-seq and microarray data for representative mRNAs in striatum and substantia nigra (SN). (JPG)

Clusters of GO biological processes and corresponding deregulated mRNAs in striatum relevant to human MSA defined by REVIGO analysis. (XLSX)

Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have been frequently shown to be deregulated in cancer. However, although several oncomiRs have been identified and characterized, there is as yet...