Kanser Enstitüsü Tez Koleksiyonuhttps://hdl.handle.net/11655/6072024-03-29T02:31:24Z2024-03-29T02:31:24ZSelection and Charaterization of İmmune-Resistant Acute Myeloid Leukemia CellsMubaida, PARVEENhttps://hdl.handle.net/11655/347482024-02-27T07:52:44Z2024-01-01T00:00:00ZSelection and Charaterization of İmmune-Resistant Acute Myeloid Leukemia Cells
Mubaida, PARVEEN
Resistance to immunity is associated with the selection of cancer cells with superior capacities to survive inflammatory reactions. In the case of AML, immune reactions induce dynamic changes at genetic and epigenetic levels, resulting in unique morphological, phenotypic, and genetic characteristics. To investigate this phenomenon, we developed an ex-vivo immune selection model, isolating residual subpopulations termed "immune-experienced" AML (ieAML) cells. Upon surviving immune reactions, these malignant blasts exhibited reduced proliferation, signs of myeloid differentiation and activation, and decreased immunogenicity. The observed low-pace proliferation, differentiation, and decreased immunogenicity were associated with immune resistance in myeloid leukemia. Furthermore, in the context of immune experience, ieAML cells displayed variations in behavior, including adhesion, migration, and polarization capacities. These immune-experienced AML subpopulations were found to impede T cell responses, resulting in reduced secretion of key anti-tumor immune response mediators. Transcriptomic analyses identified a limited set of commonly altered pathways and differentially expressed genes (DEGs) in all ieAML cells derived from various parental cell lines. Molecular signatures associated with interferon (IFN) and inflammatory cytokine signaling were enriched in AML cells resistant to T cell-mediated immune reactions. Individual ieAML lines exhibited diverse cellular responses upon subjecting them to mixed leukocyte-leukemia cell reactions (MLLRs), highlighting the variation in the regulation of similar pathways across different ieAML cell lines. Notably, distinctive traits of inflammatory pathways, such as IFN-γ, IFN-α, TNF-α, TGF-β, apoptosis, IL-6, and IL-2 signaling, were enriched. Transcription factors c-MYB and KLF6 emerged as potential markers for ieAML cells, with their expression and nuclear localization observed in subpopulations of blasts in AML patients' bone marrow aspirates. The nuclear localization of KLF6 and c-MYB transcription factors served as potential indicators of immune encounter status. Interestingly, the immune modulatory capacities of ieAML cells were transient and waned when immune selection pressure was removed. Despite this, our findings suggest that myeloid leukemia cells harbor subpopulations capable of adapting to the challenging conditions imposed by immune reactions. The prior "immune experience" of these cells may contribute to secondary resistance to immune intervention therapies. This study sheds light on the dynamics of immune interactions in AML and underscores the importance of understanding the adaptive mechanisms that cancer cells employ to escape immune surveillance.
TUBITAK, project number 120S909
2024-01-01T00:00:00ZPankreas Kanserinde Nectin-2 Ekspresyonu ile Sitotoksik T Hücre Fonksiyonları Arasındaki İlişkiGündüz, Mualla İlknurhttps://hdl.handle.net/11655/344362024-01-30T12:26:25Z2023-01-01T00:00:00ZPankreas Kanserinde Nectin-2 Ekspresyonu ile Sitotoksik T Hücre Fonksiyonları Arasındaki İlişki
Gündüz, Mualla İlknur
Checkpoint inhibitors such as anti-CTLA-4, anti-PD1 and anti-PDL-1 are used in the treatment of various cancers. However, they cannot be used in pancreatic cancer due to the lack of PDL-1 expression. Other checkpoint molecules include TIGIT family members TIGIT, CD96, DNAM-1, PVRIG. The ligands of these receptors are polio virus receptor (PVR) and Nectin family members. Nectin-2 acts as a ligand for these receptors and its role in pancreatic cancer is not fully known. The aim of this thesis is to cross-sectionally analyze the expression levels of Nectin-2 and its ligand receptors TIGIT, PVRIG, DNAM-1. In our study, the expressions of Nectin-2, CD8, TIGIT, PVRIG, DNAM-1, PD-1, PD-L1, LAG3, TIM3, VISTA, KI-67 molecules were examined in tumor tissues of 131 patients diagnosed with pancreatic cancer. Nectin-2 was not expressed in undiseased pancreatic tissue, whereas it was expressed in 30.5% of tumor tissues. PD-1 and PD-L1 expression was not observed in any of the patients. In the group with low density of CD8 TILs, the number of patients with negative Nectin-2 expression was higher than the number of patients with positive expression. In 32 patients with positive expression of Nectin-2, KI-67 proliferation marker was highly expressed. In the patient group where Nectin-2 was not expressed, the number of patients showing TIGIT expression increased. PVRIG and DNAM-1 were also not observed in the absence of Nectin-2. Patients without Nectin-2 expression had a higher number of patients without LAG3 and TIM3 expression. Nectin-2 was observed to be significantly underexpressed in stages 3 and 4 of pancreatic cancer. When the relationship between TIGIT receptor and the expression of PVRIG and DNAM-1 molecules was analyzed, a negative relationship was found and it was statistically significant. The median tumor size was 4 cm in the PVRIG positive staining group and 3 cm in the negative expression group. PVRIG and DNAM-1 positivity was more expressed in stage 2 than in stage I. There was a positive correlation between LAG3 expression and TIM3 expression. It was also observed that the presence of lymphovascular invasion increased in patients with positive LAG3 and VISTA expression. Lenf node metastasis was also significantly increased in patients with positive LAG3, TIM3 and VISTA expressions. Expression levels of VISTA molecule showed a significant difference in clinical stage 3. These data suggest that there may be a close relationship between Nectin-2 expression and the function of CD8+ cells. Further studies are needed to explain the mechanism of this relationship and to demonstrate the targetability of Nectin-2.
2023-01-01T00:00:00ZSystemıc Vh4-34-Encoded Antıbody Responses Agaınst Commensal Bacterıa in Patıents Wıth Systemıc Lupus ErythematosusKalaycı, Fatma Naz Cemrehttps://hdl.handle.net/11655/341552024-01-30T06:58:30Z2023-09-01T00:00:00ZSystemıc Vh4-34-Encoded Antıbody Responses Agaınst Commensal Bacterıa in Patıents Wıth Systemıc Lupus Erythematosus
Kalaycı, Fatma Naz Cemre
The germline immunoglobulin variable heavy chain 4–34 encoding B lymphocytes (known as VH4–34 or 9G4 B cells) are endowed with inherent self-reactivity due to the presence of a germline AVY motif in their framework region 1 of the VH4–34 gene segment. Germline self-reactive VH4-34 undergoes negative selection in the memory and plasmablast compartments of healthy donors. However, the VH4-34 censorship is compromised in systemic lupus erythematosus (SLE) patients (1), resulting in higher proportions of VH4-34 expression among plasmablasts and memory B cells.(1-3) Given the fact that gut dysbiosis and disturbances to the gut barrier integrity can set off inflammatory immune responses, and also that the association between circulating 9G4 memory B lymphocytes isolated from individuals with SLE and the gut bacteria has not been investigated to date, we seek to determine the anti-commensal bacteria reactivity of VH4-34+ IgG antibodies in SLE subjects. VH4-34 CD27+IgG+ B lymphocytes from individuals with SLE exhibit aberrant VH4-34 gene usage and display a reduction in somatic hypermutation frequencies, often with an unmutated AVY site, suggesting that their antibodies continue to possess intrinsic self-reactivity unlike their healthy donor (HD) counterparts as well as a propensity for reactivity towards commensal microorganisms. Herein, we observed that SLE VH4-34+IgG+ B lymphocytes with an unmutated AVY site exhibited an elevated level of reactivity towards gut bacteria present in the fecal samples of control groups and SLE patients, but to a smaller extent in HD stools and to a greater extent in SLE stools. Since SLE VH4-34 clonal expansion is associated with disease flare, our discovery of the SLE VH4-34 clonal expansion of gut bacteria-reactive circulating 9G4+IgG+ B cells in one SLE patient suggests that commensal bacteria translocating from the gut to the bloodstream are therefore responsible for the VH4-34 expansion in SLE. Lastly, we identified bacteria strains recognized by circulating unmutated AVY motif-encoding VH4-34-encoded antibodies, which could be attributed to a compromised intestinal barrier function in SLE patients.
2023-09-01T00:00:00ZRacial Disparity in Tumor Microenvironment and Outcomes in Residual Breast Cancer after Neoadjuvant ChemotherapyKaradal Ferrena, Burcuhttps://hdl.handle.net/11655/335452023-08-17T11:46:12Z2023-06-12T00:00:00ZRacial Disparity in Tumor Microenvironment and Outcomes in Residual Breast Cancer after Neoadjuvant Chemotherapy
Karadal Ferrena, Burcu
Black patients with residual estrogen receptor-positive (ER+) breast cancer after neoadjuvant chemotherapy (NAC) have inferior survival compared to white women resulting racial disparity in breast cancer survival. Differences in the tumor microenvironment (TME) might be one of the mechanisms behind the racial disparity in outcome. The hypothesis of this thesis study is “Racial disparity in Distant Recurrence-Free Survival (DRFS) in patients with residual ER+/ Human Epidermal Growth Factor Receptor 2 negative (HER2-) disease is due to enhanced pro-metastatic components (macrophage, microvasculature, cancer stem cell, and Tumor Microenvironment of Metastasis (TMEM) doorway density) in the tumor microenvironment post-NAC”. We stained 183 invasive ductal carcinoma tissue samples (96 Black women, 87 white women) for TMEM doorways (Pan-Mena expressing tumor cell, CD68 macrophages, and CD31 endothelial cells) and SOX9 expressing cancer stem cells (CSCs). TMEM doorway score and macrophage density were more in Black patients in the entire cohort and in the ER+/HER2- disease. TMEM doorway was an independent prognostic factor overall. There was no racial disparity in microvascular density and CSCs. In conclusion, high-TMEM doorway score was an independent prognostic factor of worse survival in patients with residual cancer post-NAC. Racial disparity in outcome might be due to an increased pro-metastatic response to chemotherapy in Black relative to white patients with residual ER+/HER2- disease.
2023-06-12T00:00:00Z