PARALKAR LAB WEBSITE: https://paralkarlab.med.upenn.edu/

RESEARCH INTERESTS

Research in the Paralkar Lab spans the spectrum from human patient sample studies and mouse models to cutting-edge molecular biology tools, high-throughput sequencing approaches, and novel computational algorithms, all with the goal of gaining insight into how ribosome biogenesis is controlled in hematopoietic stem cells, myeloid progenitors, and in leukemia, and how the transcription of noncoding ribosomal DNA genes is regulated alongside that of coding genes.

RESEARCH DETAILS

1) The Control Knob: How Does a Cell Set the Pace of Its Ribosome Factory?

Ribosomal RNA (rRNA) forms the majority of cellular RNA, and its transcription in the nucleolus by RNA Polymerase I from ribosomal DNA (rDNA) repeats accounts for the bulk of all transcription. Every cell must decide how many ribosomes to build and at what speed, and this remains one of the least studied control knobs in the cell.

In any given cell, only a fraction of its hundreds of rDNA repeats are active, and the activity of Pol I on these templates controls the rate of rRNA transcription. The Paralkar Lab built custom genomes to map this repetitive DNA, and found that many of the transcription factors that guide blood development and drive leukemia, including CEBPA, RUNX, SPI1, IRF8, and MYC, bind rDNA directly. Manipulation of several of these factors immediately impairs Pol I activity and reduces rRNA transcription.

What we are testing now: we aim to precisely map out the mechanisms underlying cell-type-specific control of ribosome numbers.

2) The Consequences: Why Do Different Blood Cells Need Different Numbers of Ribosomes?

A stem cell, a progenitor, and a mature blood cell each contain distinct numbers of ribosomes, and it is not well understood why, or to what end. The rate of ribosome production has far-reaching influence on the fate of the cell, and dictates its size, proliferation, and ability to translate global or specific mRNAs.

Across the hematopoietic tree, rRNA transcription varies approximately ten-fold, rising as stem cells commit to a lineage and falling as they mature to their final forms. Unexpectedly, these rates do not track perfectly with how much protein a cell makes or how fast it divides, suggesting that ribosome number is a regulated property in its own right, one that may help determine the fate and capacities of the cell.

What we are testing now: we aim to determine how alterations in ribosome numbers affect the ability of blood cells to maintain their homeostatic functions, and how subtle changes can affect cell states and identities.

3) The Disease: How Does Leukemia Hijack the Ribosome Factory, and Can We Selectively Repress It?

Leukemia cells have long been recognized by their characteristic prominent nucleoli, evidence of abundant ribosome production. The Paralkar Lab has shown directly that leukemic cells transcribe more rRNA and contain more ribosomes than their normal counterparts. Leukemia depends on keeping this factory in overdrive, and not only to fuel cell division: high rates of ribosome production help sustain the leukemic state itself, creating a dependence that can potentially be exploited therapeutically.

What we are testing now: we aim to define the oncogenic mechanisms that rely on high ribosome numbers, and to develop new ways of crippling ribosome production that selectively target leukemic cells while sparing normal ones.

4) Our Approach: Tools for Studying the Nucleolus and Ribosomal DNA

The nucleolus, its hundreds of near-identical DNA repeats, and the rRNAs transcribed from them have been challenging to study with standard tools. Current bioinformatic pipelines for high-throughput studies such as whole genome sequencing, RNA-seq, ChIP-seq, and single cell RNA-seq are limited in their ability to map repetitive elements of the genome like rDNA, and such loci therefore tend to be ignored in genome-wide analyses. Given that rRNA accounts for the bulk of the transcriptional output of the cell, this has created a significant knowledge gap in our understanding of the most abundant RNA in the cell.

The Paralkar Lab has built new tools to advance research in this field, working across the bench and the computer.

TEAM MEMBERS

Research staff

Postdoctoral fellows and Instructors

Graduate students

Undergraduate students