Biology subjects

Kalkat, M.

Publications and source records attributed to Kalkat, M..

3 recordsLinked to original sources

bioRxiv2025

Isolation free Identification and Phenotyping of First Trimester Extravillous Trophoblasts Residing in Cervical Fluid

Preeclampsia (PE) remains difficult to predict, particularly when it manifests late in gestation. To capture early placental signals, we profiled trophoblast cells sampled from the cervix in the first trimester using mass cytometry (CyTOF). We established protocols for clinical sample storage and applied spike-in reference control cells to deliver reproducible, batch-corrected protein measurements, thereby advancing CyTOF from a discovery tool to a translational platform. Within HLA-GCD45- cells, we identified canonical CK7 extravillous trophoblasts, as well as a previously unrecognized CK7-subset, and both subsets expressed placental proteins. Expression of PAPP-A, GAL-13, and GAL-14 was significantly altered in a pilot cohort of pregnancies that subsequently developed late-onset PE, distinguishing cases from controls at both single-marker and multivariate levels. These findings reveal unexpected trophoblast heterogeneity, demonstrate that placental alterations are detectable before the development of late-onset PE, and establish cervical trophoblast profiling as a promising platform for scalable biomarker discovery and first-trimester risk assessment in placenta-mediated disorders. Impact StatementFirst-trimester trophoblasts sampled from the cervix reveal early molecular changes associated with late-onset preeclampsia, while an isolation-free, reference-normalized CyTOF workflow establishes a scalable, clinically compatible platform for biomarker discovery and multicenter-ready early risk assessment in pregnancy.

cell biology↗

bioRxiv2022

DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

We have developed a mouse Infinium DNA methylation array that contains 297,415 probes to capture the diversity of mouse DNA methylation biology. We present a mouse DNA methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, age, sex, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This MM285 mouse array is widely accessible to the research community, and will accelerate future high sample-throughput studies in this important model organism.

genomics↗

bioRxiv2018

Modeling the MYC-driven normal-to-tumour switch in breast cancer.

The potent MYC oncoprotein is deregulated in many human cancers, including breast carcinoma, and is associated with aggressive disease. To understand the mechanisms and vulnerabilities of MYC-driven breast cancer, we have generated an in vivo model that mimics human disease in response to MYC deregulation. MCF10A cells ectopically expressing a common breast cancer mutation in the PI3 kinase pathway (PIK3CAH1047R) lead to the development of organized acinar structures in mice. However, expressing both PIK3CAH1047R and deregulated-MYC lead to the development of invasive ductal carcinoma, thus creating a model in which a MYC-dependent normal-to-tumour switch occurs in vivo. These MYC-driven tumors exhibit classic hallmarks of human breast cancer at both the pathological and molecular levels. Moreover, tumour growth is dependent upon sustained deregulated MYC expression, further demonstrating addiction to this potent oncogene and regulator of gene transcription. We therefore provide a MYC-dependent human model of breast cancer which can be assayed for in vivo tumour initiation, proliferation, and transformation from normal breast acini into invasive breast carcinoma. Taken together, we anticipate that this novel MYC-driven transformation model will be a useful research tool to both better understand MYCs oncogenic function and identify therapeutic vulnerabilities.

cancer biology↗