Biology subjects

Miglani, S.

Publications and source records attributed to Miglani, S..

5 recordsLinked to original sources

bioRxiv2025

Actionable biological programs to enhance EGFR-targeted therapy response unveiled by single-cell lineage tracing in clinically relevant lung cancer models

Developing high-resolution approaches to capture both tumor architectural clonality and transcriptional state(s) in individual cells within heterogeneous tumor cell populations could shed light on the evolution of pre-existing and newly emergent tumor subclones and their phenotypes, elucidating their trajectories in response to selective pressures such as drug treatment. Reports to date have focused primarily on analyzing the drug-induced evolution of lung cancer cells in in vitro preclinical models with limited complexity and a relative lack of characterization of actionable biological programs to induce durable responses. Here, we challenged this paradigm and employed a lineage tracing single-cell RNAseq method to track the evolution of primary non-small cell lung cancer (NSCLC) patient-derived organoids (PDOs) and tumor xenografts in response to the standard-of-care EGFR inhibitor osimertinib, with a focus on understanding drug persistence and resistance. Our single-cell lineage tracing-RNAseq system revealed the presence of a discrete set of lineages with distinct transcriptional phenotypes over the course of the treatment. We identified two lineage populations that became predominant during drug treatment and resisted therapy in the PDOs and tumor xenografts. These lineages were present before treatment and harbored Hedgehog pathway and FOXD1 transcriptional programs, respectively. These specific transcriptomic lineages were otherwise undetectable by lower-resolution profiling. Functional studies confirmed the protective role that the baseline expression of the Hedgehog pathway and FOXD1 programs in the lineage tumor cell sub-populations exerts upon targeted therapy. The potential clinical relevance of these regulatory programs was validated by cross-analysis of single-cell transcriptomic data obtained from human NSCLC specimens. Overall, our approach identified pre-existing seeds of resistance before therapy and convergent, adaptive mechanisms supporting tumor residual disease and resistant states. This study highlights the utility of high-resolution tracing of tumor clonal heterogeneity with matched single-cell profiling to reveal occult cell states and molecular mechanisms of therapy resistance and develop counteracting strategies.

cancer biology↗

bioRxiv2024

Functional screen for mediators of onco-mRNA translation specificity

Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a functional genome-wide CRISPRi screen in PDAC cells, we identified activators of selective MYC translation through its 5 untranslated region (5UTR) and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, our top hit was RBM42, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.

cancer biology↗

bioRxiv2023

Systematic Identification of Post-Transcriptional Regulatory Modules

In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we performed a systematic annotation of RBP combinatorial interactions via multimodal data integration. We built a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we used CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generated an integrated map of functional RBP interactions. We then used this map to match RBPs to their context-specific functions and validated the predicted functions biochemically for four RBPs. This study highlights the previously underappreciated scale of the inter-RBP interactions, be it genetic or physical, and is a first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

systems biology↗

bioRxiv2022

Propagated circulating tumor cells uncovers the rople of NFκB and COP1 in metastasis

Circulating tumor cells (CTCs), a population of cancer cells that represents the seeds of metastatic nodules, are a promising model system for studying metastasis. However, expansion of patient-derived CTCs ex vivo is challenging and dependent on the collection of high numbers of CTCs, which are ultra-rare. Here, we report the development of a combined CTC and CTC-derived xenograft (CDX) platform for expanding and studying patient-derived CTCs from metastatic colon, lung, and pancreatic cancers. Propagated CTCs yielded a highly aggressive population of cells that could be used to routinely and robustly establish primary tumors and metastatic lesions in CDXs. Differential gene analysis of the resultant CTC models emphasized a role for NF-kB signaling as a pan-cancer signaling pathway involved in metastasis. Furthermore, metastatic CTCs were identified through a prospective 5-gene signature (BCAR1, COL1A1, IGSF3, RRAD, and TFPI2). Whole-exome sequencing of CDX models and metastases further identified mutations in constitutive photomorphogenesis protein 1 (COP1) as a potential driver of metastasis. These findings illustrate the utility of the combined patient-derived CTC model and provide a glimpse of the promise of CTCs in identifying drivers of cancer metastasis.

cancer biology↗

bioRxiv2021

An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus

Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis, however its effects on cancer progression remain poorly understood. To address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed novel regression-based methods to analyze ribosome profiling and alternative polyadenylation data, and identified HNRNPC as a translational controller of a specific mRNA regulon. Mechanistically, HNRNPC, in concert with PABPC4, binds near to poly(A) signals, thereby governing the alternative polyadenylation of a set of mRNAs. We found that HNRNPC and PABPC4 are downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3 UTR lengthening and subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. We also found that a small molecule, previously shown to induce a distal-to-proximal poly(A) site switching, counteracts the HNRNPC-PABPC4 driven deregulation of alternative polyadenylation and decreases the metastatic lung colonization by breast cancer cells in vivo.

cancer biology↗