Of necessity, cancer cells are usually studied at a single time point, when a tumor is excised.

Cancer cells cultured in petri dishes can be looked at over time, allowing a far better understanding of "short or long term" changes, perhaps even differentiation. In a series of ten papers, we have described morphological sequences that allow a better understanding of changes in endometrial epithelial cells that are differentiating into typical epithelial structures such as domes and gland-like structures that arise from domes.

For example, the so-called "optically clear" nuclei, frequently observed in cancer tissue were a mystery for a couple of decades. More is known about what they signify now that it has been possible to study them in vitro where it has been found that such structures are part of the process of dome/gland formation. (Fleming H. 1999)

Among the complex structural changes induced by a factor in fetal calf serum during differentiation of domes or hemicysts are chromatin aggregates in syncytium that become vacuolated as shown in fig. 1. These structures closely resemble the "optically clear nuclei" (OCN) found in some cancers.

In addition to the vacuole(s), optically clear nuclei are also characterized as structures that stain for endogenous biotin, a result that initially caused confusion and consternation: consternation because biotin linked antibodies are so frequently used for detection of specific proteins; confusion because most of the biotin in a cell is linked to carboxylases containing the coenzyme biotin and functional in mitochondria, almost exclusively.

Sampling of research papers describing optically clear nuclei over a couple of decades:

Biotin-rich intranuclear inclusions in morule-lacking adenocarcinoma of the gallbladder: a new category of "neoplastic/non-morular" lesions. Kimura Y, Kashima K, Daa T, Kondo Y, Yada K, Sasaki A, Matsumoto T, Kitano S, Kubo N, Yokoyama S. Virchows Arch. 2005 Feb;446(2):194-9. Epub 2005 Jan 13.

Biotin-rich, optically clear nuclei express estrogen receptor-beta: tumors with morules may develop under the influence of estrogen and aberrant beta-catenin expression. Nakatani Y, Masudo K, Nozawa A, Inayama Y, Yamanaka S, Ito T, Kitamura H, Notohara K, Kashima K, Yokoyama S, Tsujimoto M, Tamai S, Abe Y, Resl M, Mark EJ. Hum Pathol. 2004 Jul;35(7):869-74.

**Aberrant intranuclear localization of biotin, biotin-binding enzymes, and beta-catenin in pregnancy-related endometrium and morule-associated neoplastic lesions. Gamachi A, Kashima K, Daa T, Nakatani Y, Tsujimoto M, Yokoyama S. Mod Pathol. 2003 Nov;16(11):1124-31 (An enlightening systematic analysis of 17 neoplastic lesions with morules showed that nuclei in every instance were associated with biotin linked to mitochondrial carboxylases. Researchers also found optically clear nuclei in "normal" endometrium).

Pancreatoblastoma. A case report with special emphasis on squamoid corpuscles with optically clear nuclei rich in biotin. Hasegawa Y, Ishida Y, Kato K, Ijiri R, Miyake T, Nishimata S, Watanabe T, Namba I, Hayabuchi Y, Kigasawa H, Tanaka Y. Acta Cytol. 2003 Jul-Aug;47(4):679-84

Morules with optically clear nuclei in ovarian borderline endometrioid tumor. Li CC, Hirokawa M, Qian Z, Fujii Y, Ino H, Wakatsuki S, Horiguchi H, Kagawa N, Sano T.APMIS. 2002 Nov;110(11):783-8

Morules with biotin-containing optically clear nuclei in colonic tubular adenoma.Sasaki A, Yokoyama S, Arita T, Inomata M, Kashima K, Nakayama I.Am J Surg Pathol. 1999 Mar;23(3):336-41

Pancreatoblastoma: optically clear nuclei in squamoid corpuscles are rich in biotin.Tanaka Y, Ijiri R, Yamanaka S, Kato K, Nishihira H, Nishi T, Misugi K.Mod Pathol. 1998 Oct;11(10):945-9

Morule with biotin-containing intranuclear inclusions in thyroid carcinoma.Okamoto Y, Kashima K, Daa T, Yokoyama S, Nakayama I, Noguchi S.Pathol Int. 1995 Aug;45(8):573-9

Pulmonary endodermal tumor resembling fetal lung. The optically clear nucleus is rich in biotin. Nakatani Y, Kitamura H, Inayama Y, Ogawa N. Am J Surg Pathol. 1994 Jun;18(6):637-42.

Optically clear and vacuolated nuclei. Two useful signs for the transoperative diagnosis of papillary carcinoma of the thyroid. Dominguez-Malagon HR, Szymanski-Gomez JJ, Gaytan-Garcia SR. Cancer. 1988 Jul 1;62(1):105-8.

Optically clear endometrial nuclei. Sobel HJ, Marquet E, Schwarz R, Mazur MT.Ultrastruct Pathol. 1984;6(2-3):229-31.

Optically clear nuclei. An alteration of endometrial epithelium in the presence of trophoblast. Mazur MT, Hendrickson MR, Kempson RL. Am J Surg Pathol. 1983 Jul;7(5):415-23.

The optically clear nucleus. A reliable sign of papillary carcinoma of the thyroid? Hapke MR, Dehner LP. Am J Surg Pathol. 1979 Feb;3(1):31-8

Intimate association of mitochondrial membranes with chromatin can explain detection of endogenous biotin in cross sections of optically clear nuclei. Association may also be responsible for generation of a gas or of a mixture of gases into chromatin mass. Candidates for identity of gas include CO2 and NO. A bubble of NO gas is generated in stressed HeLa cells. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950269/

Origins of optically clear nuclei based on observations of differentiating endometrial epithelial cancer cells in vitro.

OCN, an acronym for cells with chromatin containing one or more vacuoles, are not a type of epithelial cell but a stage in differentiation of monolayer epithelial cells into domes and, under appropriate conditions into gland-like structures.

"Optical clearing" results from the generation of gas vacuoles into chromatin at the center of a mitonucleon.

Gases generated into chromatin may activate enzymes that bring about changes in chromatin structure essential for formation of glands.

The second page discusses how optically clear nuclei (OCN) elevate off the dish to become signet ring cells.