Chowdhury Lab Research
Basic Mechanisms of Genome Stability
The integrity of the genome is constantly challenged by DNA damage and replication stress, which together drive tumorigenesis and influence therapeutic response. Our research program focuses on dissecting the molecular mechanisms that maintain genome stability, while uncovering new regulatory axes and therapeutic vulnerabilities. Five interconnected projects—on BRCA1, ATR, CDK5, TIRR, and MRE11/DYNLL1—anchor this effort.
BRCA1-dependent ubiquitination in DSB repair and replication
BRCA1 is a central tumor suppressor, classically defined by its essential role in homologous recombination (HR). However, whether its intrinsic E3 ubiquitin ligase activity meaningfully contributes to genome stability has been debated for decades. Some studies suggested BRCA1-mediated ubiquitination was dispensable for repair and tumor suppression, while others reported context-specific functions, creating a persistent controversy. Our work provides evidence that BRCA1/BARD1-dependent ubiquitination represents a distinct regulatory pathway, separate from BRCA1’s direct catalytic role in HR, that influences repair pathway choice and replication fork dynamics. This redefines BRCA1’s molecular scope, establishing ubiquitination as a physiologically important activity. The outstanding questions now are: which proteins are bona fide substrates of BRCA1/BARD1 ubiquitination? How does this modification control their activity at DNA breaks and replication forks? Can such events serve as biomarkers of therapeutic response, or as druggable vulnerabilities in BRCA-driven cancers? By resolving this controversy, we not only clarify BRCA1 biology but also reveal new entry points for therapy in replication-stressed tumors.
ATR and replication stress tolerance pathways
Replication stress is a universal hallmark of cancer and a major source of therapeutic vulnerability. ATR kinase is the master regulator of the replication stress response, yet its essential role in normal cells raises the puzzle of why ATR inhibitors (ATRi) are well tolerated clinically and exhibit tumor-selective effects. Our discovery of DNAJC9, a previously uncharacterized factor in effective pre-replicative complex formation, uncovered a critical determinant of ATR dependency. Loss of DNAJC9 delays S-phase entry and creates acute hypersensitivity to ATRi, suggesting that the link between replication origin licensing and ATR signaling is central to stress tolerance. Despite this insight, key questions remain: how does ATR signaling intersect with origin licensing selection to buffer stress? Why are some tumors exquisitely sensitive to ATRi while others are resistant, and do these differences reflect reliance on ETAA1- versus TOPBP1-mediated ATR activation? Which replication stress response proteins dictate ATRi sensitivity, and can they be exploited as predictive biomarkers? By addressing these questions, we aim to sharpen the therapeutic use of ATR inhibitors and uncover fundamental principles of how human cells manage replication stress.
CDK5 as a mitotic kinase and therapeutic target
Cyclin-dependent kinase 5 (CDK5) has long been regarded as an atypical kinase restricted to neuronal biology. Our studies redefined CDK5 as a bona fide mitotic regulator: it partners with cyclin B1, safeguards chromosome segregation, and also localizes to replication forks where it controls fork dynamics and replisome phosphorylation. CDK5 loss slows fork movement identifying it as a new determinant of replication stress tolerance. Recently, we solved the first high-resolution crystal structures of the CDK5–cyclin B1 complex, which revealed canonical features of mitotic cyclin-CDK assembly missed by AI-predicted models. These structural insights now enable rational drug discovery, opening the door to selective molecular glue degraders that target unique CDK5–cyclin B1 interfaces, rather than conventional ATP-competitive inhibitors. Key questions now include: why do cells require both CDK1–cyclin B1 and CDK5–cyclin B1 complexes for mitotic fidelity? Does CDK5 uniquely shape replication stress responses and ATR dependency? Can phosphorylation of substrates such as PARP1 connect CDK5’s dual roles in replication and repair? And will molecular glues against CDK5 unlock therapeutic selectivity in proliferative cancers like ovarian carcinoma? Together, these advances place CDK5 at the crossroads of replication, mitosis, and therapeutic vulnerability.
TIRR as a brake on p53 activation
The tumor suppressor p53 is often inactivated in cancer, either by mutation or by silencing of its activity. We discovered TIRR (Tudor Interacting Repair Regulator) as an unexpected, endogenous brake on p53. TIRR restrains p53 activity through two mechanisms: masking the Tudor domain of 53BP1 to regulate p53’s chromatin engagement and functioning as an RNA-binding protein that destabilizes a subset of p53-induced transcripts. Loss of TIRR in mice selectively activates p53 without developmental toxicity, a striking finding that distinguishes it from toxic MDM2/MDM4 inhibitors. Furthermore, clinical data show that low TIRR levels correlate with improved outcomes in p53-heterozygous tumors. These results nominate TIRR as a new therapeutic target for cancers that retain wild-type p53 but silence its function. Our studies using PRO-seq and iCLIP-seq reveal TIRR’s dual transcriptional and post-transcriptional functions, but key questions remain: how is the TIRR–53BP1–p53 complex dynamically regulated under different forms of stress? Which p53 targets are governed primarily at the transcriptional versus post-transcriptional level? Can acute pharmacologic disruption of TIRR reproduce the beneficial, non-toxic p53 activation seen in genetic knockouts? And which tumor contexts rely most heavily on TIRR-mediated suppression of p53? Answering these questions could unlock a selective and tractable way to restore p53 tumor suppression in human cancers.
DYNLL1 as a regulator of MRE11
MRE11, the evolutionarily conserved nuclease core of the MRN complex, is indispensable for DSB repair and replication fork metabolism. Yet unchecked MRE11 activity is genome-destabilizing, leading to pathological resection and fork collapse. Our work identified DYNLL1 as a bona fide cellular inhibitor of MRE11, the first endogenous mechanism that directly restrains MRE11 activity in cells. By binding and destabilizing MRE11 dimers, DYNLL1 limits nuclease function, controls pathway choice, and influences therapeutic responses, particularly in BRCA1-deficient cancers. This discovery reframed MRE11 regulation as an active, tunable process rather than a passive balance of repair factors. However, major open questions remain: How is MRE11 recruited to chromatin in the absence of exogenous damage? What signals determine its timely release, and how do phosphorylation, ubiquitination, or other post-translational modifications coordinate with DYNLL1 to regulate its stability and activity? And fundamentally, how do cells decide when MRE11 activity is protective versus destructive? Understanding these mechanisms will illuminate how replication and repair are integrated and may reveal therapeutic windows to modulate MRE11 activity in repair-deficient tumors.
Integrative Perspective
Although each project is anchored in a distinct molecular axis—BRCA1 ubiquitination, ATR replication stress signaling, CDK5 mitotic control, TIRR-mediated p53 suppression, and DYNLL1 regulation of MRE11—they converge on a unifying theme: genome stability is not maintained by core machineries alone, but by a network of regulatory factors that tune these machineries to balance protection and risk. By defining how these axes operate in replication, repair, and checkpoint contexts, our work not only addresses long-standing mechanistic controversies but also opens new therapeutic directions in cancers that exploit replication stress and repair defects.
Translational Research- circulating miRNAs as biomarkers for human pathology
Of the many classes of circulating nucleic acids, miRNAs are remarkably stable against various physiological and physical conditions, and are readily detectable and quantifiable by rapid and sensitive PCR approach in a high throughput manner. These characteristics of miRNAs rendered them ideal noninvasive biomarkers for various pathological conditions. We are focusing on identifying and establishing miRNA expression signatures as potential diagnostic tools for the following clinical challenges:
Circulating miRNAs as Biomarkers of Hereditary Cancer Risk
Our work has shown that circulating microRNAs (miRNAs) can identify individuals carrying germline BRCA1/2 mutations, even in the absence of cancer. These signatures not only distinguish carriers but also predict future ovarian cancer risk, providing a functional readout of “BRCAness” that symbolizes homologous recombination deficiency. This raises a broader question: can similar miRNA profiles capture mismatch repair defects? We are now extending this approach to Lynch Syndrome, where mutations in mismatch repair genes confer high lifetime risks of colorectal, endometrial, and other cancers. Just as BRCA deficiency is marked by a distinct miRNA footprint, we ask whether mismatch repair deficiency generates its own detectable circulating signature. If validated, this strategy could establish circulating miRNAs as a generalizable biomarker platform for hereditary cancer syndromes, enabling earlier detection, improved risk prediction, and more precise prevention strategies.
Circulating miRNAs for Early Detection of Ovarian Cancer
Ovarian cancer is among the most lethal gynecologic malignancies because it is usually diagnosed late, when effective treatment options are limited. While the overall five-year survival rate across all stages is only ~47%, women diagnosed when the disease is confined to the ovary have a survival rate exceeding 90%. This striking difference highlights the critical need for reliable early detection tools. Our work has focused on circulating miRNAs as a non-invasive biomarker platform. Although only ~10% of miRNAs are found in blood, they retain tissue specificity, allowing a blood test to provide insight into tumor biology. Using small RNA sequencing and advanced modeling, we identified serum miRNA signatures that can accurately distinguish invasive ovarian cancers from benign and borderline tumors. These profiles capture molecular signals of malignant transformation and, in recent iterations, have detected 100% of stage I and stage II–IV epithelial ovarian cancers, with overall sensitivity of 96% and specificity of 95%. We are now working to translate these findings into clinical application. The current test—developed in collaboration with Aspira Women’s Health and branded as OVAinform—has consistently detected 90–92% of ovarian cancers with strong specificity across independent sample batches. By refining these assays and validating them in prospective studies such as the MiDe Study, our goal is to bring forward a cost-effective, accurate blood test that can fundamentally change ovarian cancer prevention, detection, and survival.
Radiation and Circulating miRNAs
Radiation exposure—whether from accidents, terrorism, or medical treatment—poses major risks to human health, yet current tools cannot predict the severity of organ-specific injury. We have identified circulating miRNA signatures that respond to radiation and predict long-term hematopoietic injury in mice, with conservation across non-human primates and evidence in cancer patients receiving radiotherapy. These findings suggest circulating miRNAs could serve as non-invasive biomarkers to guide organ-targeted treatment after radiation exposure. Distinct miRNA patterns also correlate with radiation dose and timing, supporting their use in predicting survival and informing timely medical response. Finally, since radiation therapy itself can induce secondary cancers, especially in pediatric patients, we are defining serum miRNA profiles that could identify susceptibility to therapy-induced malignancies early in the treatment course, improving long-term outcomes and quality of life.
