Research
Research focus: Nuclear Architecture and Cancer
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Chromosome Biology Lab
Spectral Karyotyping (SKY) of a metaphase spread from DLD1 colorectal cancer cells (A) DAPI staining of a metaphase spread (B) Raw colors from a SKY hybridization on a metaphase (C) pseudocolors to classify each chromosome
Role of nuclear Lamins in regulating chromosome territory organization How are chromosome territories organized in the interphase nucleus? Genomics approaches such as Hi-C, further substantiate that the genome is non-randomly organized in the nucleus. Here we addressed the role of nuclear Lamins in regulating nuclear structure and function in cancer cells. These studies revealed that while lamin depletion did not perturb the localization of most chromosome territories. Lamin loss induced chromosomal aneuplodies in diploid colorectal cancer cells. Interestingly, the nuclear locations of the aneuploid chromosomes were altered in the interphase nucleus. Furthermore, gene expression analyses of Lamin depleted cells also showed a significant extent of transcriptional deregulation. Ongoing project: The focus is to investigate into the underlying mechanisms by which Lamins and Lamin B Receptor (LBR) regulates chromosomal stability in colorectal cancer cells. Ref: Ranade D, Koul S, Thompson J, Prasad KB and Sengupta K (2016) Chromosomal aneuploidies induced upon Lamin B2 depletion are mislocalized in the interphase nucleus. Chromosoma. 1-22.
2. Mechanisms that regulate nucleolar morphology and function in cancer cells Here we examined the mechanisms that regulate the morphology and function of the nucleolus. Our studies showed the interesting role of nuclear lamin B2, in regulating nucleolar morphology, since the knockdown of Lamins resulted in aggregates of the nucleoli in the interphase nucleus. Ref: Sen Gupta A and Sengupta K. Ongoing project: Functional characterization of nuclear lamins in nucleolar organization in cancer cells. Lamin B2 modulates nucleolar morphology, dynamics and function. Mol. Cell. Biol 2017.
Immunofluorescence staining of Nucleolin (red) shows nucleolar aggregates in the nucleus (DAPI, blue) of colorectal cancer cells upon Lamin B2 knockdownSen Gupta A & Sengupta K MCB, 2017.
Nucleoporins and their association with chromatin The nuclear pore complex regulates the entry and exit of molecules to and from the nucleus. In addition, nuclear pore proteins bind to DNA and regulate gene expression. We showed that Nup93 associates with chromatin dependent on its interactors Nup188 and Nup205, and represses the HOXA gene cluster. Furthermore, Nup93 and CTCF associate with the 3' and 5' regions of the HOXA gene cluster and modulate its expression in undifferentiated cells. Ref: Labade AS, Karmodiya K, Sengupta K. Ongoing project: We are currently investigating into the role of Nup93 sub-complex in regulating de-differentiation. HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205. Epigenetics Chromatin. 2016, Dec 3;9:54
A cartoon representation depicting the status of the HOXA gene cluster in undifferentiated cells. The HOXA gene locus is poised for expression, and shows a significant increase and decondensation upon Retinoic Acid (RA) treatment. HOXA cluster is re-condensed and silenced in differentiated cells. Labade et al, July, 2019, BioRXiV.
4. Chromosome organization in cells on softer matrices: Chromosome territory positions are altered within ~90 mins in an emerin-lamin dependent mechanism. We showed that emerin is phosphorylated when cells are on softer matrices. Interestingly, inhibition of emerin phosphorylation via PP2 (SRC Kinase inhibitor) or emerin (Y99F) abrogrates movement of chromosome territories in cells on softer matrices. Ref: Pradhan R, Ranade D and Sengupta K. Ongoing project addresses mechanisms of chromosome territory position and function when challenged with various mechanical signals. Emerin modulates spatial organization of chromosome territories in cells on softer matrices. Nucleic Acids Res. 2018.
A cartoon representation of mechanochemical signals that are relayed from the extracellular matrix into the cell by the cytoskeletal network into the nuclear envelope via emerin and lamins proteins, resulting in altered chromosome territory positions and gene expression.
5. Role of nuclear architecture in gene expression regulation of cancer cells Epithelial to Mesenchymal Transitions (EMT) is a key process in early development, wherein cells transition from the epithelial to the mesenchymal state. EMT is also a hallmark of cancer progression as it facilitates metastasis. Here we induced EMT by treating A549 lung cancer cells with TGF-B. In addition to EMT induction, these cells shows distinctive changes in cell morphology with a marked increase in actin stress fibres. Our ongoing experiments aim to address the impact of EMT on chromosome organization and transcription. Ongoing project: Investigates into the functional characterisation of two independent inducers of EMT namely TGF-B and Twist1 in modulating EMT and genome organization in cancer cells.
EMT induction in A549 lung cancer cells by TGF-B treatment, also enhances actin stress fibres.
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