Single Cell Omics, Stockholm May 26th

Branching developmental pathways through high dimensional single cell analysis in trajectory space: application to the tumor environment and tumor control of the immune response

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Cancer immunotherapy has proven successful with new generations of drugs (e.g. checkpoint inhibitors) that target lymphocytes and their surface molecules, however only small fraction of the patients benefits from these drugs. Thus, it is important to uncover additional mechanisms of tumor immune evasion. Lymphocytes are recruited into tumor by endothelial cells (ECs), which are the interface between the tumor and circulating blood. Tumors induce specialized ECs, known as high endothelial venules (HEV). Induction of HEVs in tumors correlates with favorable prognosis, but many tumors use HEVs to recruit immune suppressive cells. Tumor microenvironment through conditioning of the local endothelium trafficking programs mediates recruitment of immune suppressive lymphocytes and enhances carcinogenesis. Interaction of tumors may also alter the imprinting of lymphocyte adhesion/trafficking programs in tumor draining lymph nodes (LN) either through effects on tumor derived dendritic cells or directly when the LN is invaded by metastatic cells. We take advantage of mass cytometry (CyTOF) and single cell RNA-Seq to monitor the induction and regulation of EC and leukocyte trafficking receptors in B16, B16 OVA (more immunogenic), 4T1 and colon mouse tumors. High dimensional data, rich in information, is analyzed using an innovative single cell analysis algorithm, which aligns cells in developmental trajectories using protein or gene expression(s) of single cells. This algorithm has the potential to reveal, for the first time in an unsupervised manner, complex branching and allows the detection of new functionally important cells or specific transient cell populations. #Ksomics

Mutator phenotype versus growth advantage in cancer

I’ve been fascinated by DNA and genetics since reading Jurassic park as a kid. Later, when I started with studies I couldn't wait until I was ready to engage in actual course on genetics. At that time my attention was drawn to DNA mismatch repair (MMR). A highly conserved mechanism, which exists in every alive cell and its primary role is to detect mismatches in DNA that will become mutations if not corrected prior cell divides.

Mismatch repair mechanism consist of rather simple steps. First, MSH2-MSH6 detect mismatch. Second, MLH1-PMS2 is engaged and that signals EXOI to cut out mismatch. New gap in DNA strand is re-sythetized by DNA polymerase.

Mismatch repair mechanism consist of rather simple steps. First, MSH2-MSH6 detects mismatch. Second, MLH1-PMS2 is engaged and that signals EXOI to cut out mismatch. New gap in DNA strand is re-sythetized by DNA polymerase.

Taken high conservation from bacteria to humans, somebody would say if you mess up with MMR life would not be possible, but… none of MMR genes when inactivated are lethal, nevertheless inactivation of even just one of two gene copies will speed up cancer development. A syndrome named after Henry Lynch is associated with inherited mutations in MMR genes. Individuals with inherited mutations in MMR genes have predisposition to develop mainly gastrointestinal cancers and women endometrial cancer.

Why is that? Well, many would say isn’t it obvious? Deficient mismatch repair leads to increased mutation rate which at the end causes cancer. I encounter this answer again and again. But increased mutability isn’t necessarily a bad thing. Without mutations life wouldn’t evolve. So why is it then that MMR deficiency is a shortcut to cancer? A less known function of MMR, and quite often shadowed by mutator phenotype, is its role in signalling apoptosis or cell death.

Healthy cells when faced with irreparable mismatch, and DNA damage in general, will either enter senescence (something like retirement, cell is still alive but not dividing anymore), or undergo apoptosis - death. MMR deficient cells, will gather more mismatches because of obvious reasons, but these cells will not undergo senescence neither trigger apoptosis. They will divide and mismatches will become mutations, of which some mutation combinations will be lethal for cell, some will live. The latter is just matter of statistics and combinatorics which combination will evolve into cancer.

In other words, inactive MMR is a shortcut to cancer because MMR deficient cells have selective growth advantage over healthy cells, and mutator phenotype is just speeding variability of cells.

Most chemotherapeutic drugs work on principle to induce apoptosis in cancer cells, but that strategy does not work in MMR deficient cancer cells, because they are unable to signal apoptosis. At present moment only gene therapy, which would restore MMR activity, accompanied by cytostatic would be efficient approach. In light of not-that-successful experiments and quite high risks of gene therapy, my opinion is that understanding mechanisms by which MMR signals apoptosis in greater detail would give a clue towards new drugging aproaches for MMR deficient cancers.