Nonlinear optical imaging and Raman microspectrometry of the cell nucleus throughout the cell cycle

Abstract

Fundamental understanding of cellular processes at molecular level is of considerable importance in cell biology as well as in biomedical disciplines for early diagnosis of infection and cancer diseases, and for developing new molecular medicine-based therapies. Modern biophotonics offers exclusive capabilities to obtain information on molecular composition, organization, and dynamics in a cell by utilizing a combination of optical spectroscopy and optical imaging. We introduce here a combination of Raman microspectrometry, together with coherent anti-Stokes Raman scattering (CARS) and two-photon excited fluorescence (TPEF) nonlinear optical microscopy, to study macromolecular organization of the nucleus throughout the cell cycle. Site-specific concentrations of proteins, DNA, RNA, and lipids were determined in nucleoli, nucleoplasmic transcription sites, nuclear speckles, constitutive heterochromatin domains, mitotic chromosomes, and extrachromosomal regions of mitotic cells by quantitative confocal Raman microspectrometry. A surprising finding, obtained in our study, is that the local concentration of proteins does not increase during DNA compaction. We also demonstrate that postmitotic DNA decondensation is a gradual process, continuing for several hours. The quantitative Raman spectroscopic analysis was corroborated with CARS/TPEF multimodal imaging to visualize the distribution of protein, DNA, RNA, and lipid macromolecules throughout the cell cycle.

Figure 1

Concentration analysis of Raman spectra acquired in the labeled domains of the cell nucleus and in mitotic cell. The Raman spectra were acquired in the major subnuclear domains, and in the mitotic chromosomes and extrachromosomal regions of the mitotic cells. The DNA transcription sites (TS), nuclear speckles, nucleoli, and domains of constitutive heterochromatin were visualized in the fixed cells (data shown on A–D) by the immunofluorescent labeling of nascent transcripts, splicing factor SC-35, nucleolar protein nucleolin, and centromeric protein B (CENPB), respectively, using Alexa-488 conjugate. The mitotic chromosomes were visualized in live cells (data shown on E and F) by either acridine orange staining or in the transmission light. The presented spectra were averaged from 10 measurements for each type of site in the cell nucleus or in the mitotic cell. (A) (Top chart) The averaged Raman spectrum of TS is shown in solid representation. The model of TS spectrum, generated as the best proportion match of weighted spectral sum of the concentration calibrated reference spectra of DNA, RNA, proteins, and lipids, is shown in shaded representation. (Bottom chart) The difference between the model spectrum and the averaged spectrum acquired from TS. The subtraction result indicates a close match of a model to the actual spectrum measured in TS. (B–E) (Top charts) Raman spectra (shading) in nuclear speckles (B), nucleoli (C), centromeric heterochromatin domains (D), mitotic chromosomes (E), and the Raman spectrum of TS (solid representation). (Bottom charts) Overlays of the differential spectra of the corresponding site and the spectrum of TS (solid representation) and the generated models (shading) used for quantitative assessment of the spectra difference. (F) (Top chart) The Raman spectrum of extrachromosomal regions of mitotic cell (solid representation) and the spectrum of mitotic chromosomes (shading). (Bottom chart) The difference of the Raman spectra of extrachromosomal regions and the Raman spectrum of mitotic chromosomes; and overlay with the model spectrum difference simulation (shading). The averaged concentrations of DNA, RNA, proteins, and lipids in the nuclear domains and mitotic cells, derived from model spectra analysis (diagrams at the right). The concentration is given in mg/mL. (Error bars) Experimental errors.

Figure 2

Dynamics of DNA concentration throughout the cell cycle. Presented spectra are averaged from 10 independent measurements. (A) Raman spectra acquired in live cells on mitotic chromosomes or in interphase nuclei synchronized in G1, early, mid, and late S/G2-phase. The intensity peak used for measurement of the DNA concentration (red outline) was enlarged and rescaled (left corner). (B) DNA concentration dependence on time. Cells were acquired during the mitosis (0 min) and averaged 70, 300, 400, 650, and 1000 min after the completion of mitosis. (C) The BrdU incorporation pattern confirms the synchronization of the last three time points to the early, mid, and late S-phase. (D) The volume of the cell nucleus averaged in early and late S-phase. (Error bars) Standard deviation.

Figure 3

Multimode TPEF/CARS images of the live mitotic and interphase cell obtained in a single scan. Imaging was performed in live cells. (A–H) Images of proteins (A and E), lipids (B and F), DNA (C and G), and RNA (D and H) in mitotic and interphase cells, respectively. Proteins and lipids were visualized by CARS and DNA and RNA by selective staining with acridine orange. During mitosis, proteins were organized into a complex structure covering the entire cell. Accumulations of proteins in the center of the dividing cell were seen (arrowheads). Bright focal accumulations of the proteins and lipids at the periphery of mitotic cells were frequently observed (arrows). In the interphase nucleus, the strongest protein signal corresponds to the nucleolus (arrow). Lipids are accumulated in the nuclear envelope (arrow) and the lipid droplets in cytoplasm (arrowhead). The strongest RNA signal corresponds to the nucleolus (arrow). (I and J) Enlarged images of mitotic and interphase cells with merged signals from proteins (red), lipids (green), and DNA (blue). In the mitotic cell protein clusters, partially overlapping mitotic chromosomes are seen (arrows in I). In the interphase cell, a line profile crosses a condensed perinucleolar chromatin (arrowheads in J). (K and L) Signal intensity line profile through mitotic cell (K) and interphase cell nucleus (L), with DNA (blue), proteins (red), and lipids (green). (Arrowheads) Indication that an increase in DNA compaction does not correlate with an increase in the proteins' signal. (Scale bars) 5 μm.