Biology subjects

Chijioke, O.

Publications and source records attributed to Chijioke, O..

7 recordsLinked to original sources

bioRxiv2026

MTAP deficiency is a novel biomarker in neuroendocrine neoplasms of the lung

IntroductionMTAP emerges as potential predictive biomarker for MTA-cooperative PRMT5-inhibitors. Although MTAP attracts increasing attention in non-small cell lung cancer, its role in pulmonary neuroendocrine neoplasms (NENs) remains largely unexplored. MethodsHere, we assessed the prevalence of MTAP deficiency in 209 pulmonary NENs using immunohistochemistry (IHC). Additionally, we performed fluorescence in situ hybridization (FISH), whole exome sequencing (WES), deep proteomic profiling, transcriptomic, and methylation analyses of selected MTAP deficient and proficient carcinoids to further elucidate the underlying mechanisms of MTAP expression pattern. ResultsMTAP deficiency by IHC was detected in all neuroendocrine precursor lesions (n=17), 92% of typical carcinoids (n=51), 86% of atypical carcinoids (n=21), and 10% of large cell neuroendocrine carcinomas (LCNEC) (n=30). In contrast, all small cell lung cancers (SCLC) were MTAP proficient (n=90). In MTAP deficient carcinoids, FISH and WES did not detect homozygous 9p21 deletions, and methylation analysis showed no evidence of MTAP promoter hypermethylation. Comparing MTAP deficient and MTAP proficient carcinoids, proteomic data showed a clear separation between the two groups. Further, there was an inverse correlation between the expression of MTAP and OTP (orthopedia homeobox protein), which is known as a strong prognostic marker in pulmonary carcinoids. DiscussionMTAP deficiency is a novel hallmark of neuroendocrine precursors and most pulmonary carcinoids, clearly distinguishing the latter from SCLC and most LCNEC. It is neither caused by 9p21 deletion, nor by MTAP promoter hypermethylation. MTAP deficiency is a group-defining feature of carcinoids that might pave the way for new therapeutic approaches.

pathology↗

bioRxiv2025

A high-resolution, unbiased analysis of the cellular immune response to Epstein-Barr virus

More than 95% of humans are infected with Epstein-Barr virus (EBV), yet although EBV infection has been associated with inflammatory and autoimmune diseases, lymphoproliferative disorders, and several types of cancer, for the vast majority of infected people the infection is asymptomatic as EBV replication is controlled by the immune system. Immunity against this virus has been studied since the discovery of EBV in the 1960s, and although important insights have been made, no unbiased, global studies of immune responses to EBV in healthy seropositive subjects have been reported. Here we describe a novel protocol to study the cellular immune response to EBV, detecting lymphocytes that respond to EBV via analyses of proliferation or induced expression of activation markers and cytokines. Using this system we sequenced, for the first time at a single-cell level, the transcriptome of all cells capable of responding to EBV in healthy individuals and in patients with inborn errors of immunity (IEI) associated with susceptibility to EBV infection. Lymphocyte cytotoxicity appears to be crucial for the proper control of EBV-infection, while a proportionate T-regulatory cell response likely helps to avoid excessive immunity and immune pathology. We also show that {gamma}{delta} T cells expressing the TCR V{delta}1 chain use various activating natural killer (NK) cell receptors to recognise and kill EBV-infected lymphoblastoid cell lines (LCLs) and thus could be a promising candidate for allogeneic cell therapy for EBV-associated lymphoproliferative disorders in patients with either primary or secondary immunodeficiencies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/681317v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@116ad85org.highwire.dtl.DTLVardef@1da33d7org.highwire.dtl.DTLVardef@81a2a6org.highwire.dtl.DTLVardef@dd571d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

IGLV3-21-R110-directed bispecific antibodies activate T cells and promote killing in a high-risk subset of chronic lymphocytic leukemia

We previously used a disease-specific B cell receptor (BCR) point mutation (IGLV3-21R110) for selective targeting of a poor-risk subset of chronic lymphocytic leukemia (CLL) with chimeric antigen receptor (CAR) T cells. Since CLL is a disease of the elderly and a significant fraction of patients is not able to physically tolerate CAR T cell treatment, we explored bispecific antibodies as an alternative for precision targeting of this tumor mutation. Heterodimeric IgG1-based antibodies consisting of a fragment crystallizable region (Fc) attached to either an anti-IGLV3-21R110 Fab or an anti-CD3 (UCHT1) single chain variable fragment (R110-bsAb) selectively killed cell lines engineered to express high levels of the neoepitope as well as primary CLL cells using healthy donor and CLL patient-derived T cells as effectors. R110-bsAb spared polyclonal human B cells (as opposed to CD19-targeting Blinatumomab) as well as CD34+ human stem cells. Yet, R110-bsAb induced lower T cell activation than Blinatumomab with primary CLL cells likely due to lower expression of target antigen. In vivo, R110-bsAb specifically killed IGLV3-21R110-expressing cell lines and CLL cells while sparing peripheral blood mononuclear cells. These findings highlight bispecific antibodies as a promising, off-the-shelf immunotherapy for high-risk CLL patients, offering selective targeting while preserving healthy B cells.

cancer biology↗

bioRxiv2023

Epstein Barr virus infection induces tissue-resident memory T cells in mucosal lymphoid tissues

Epstein Barr virus (EBV) contributes to around 2% of all tumors worldwide. Simultaneously, more than 90% of healthy human adults persistently carry EBV without clinical symptoms. In most EBV carriers it is thought that virus-induced tumorigenesis is prevented by cell-mediated immunity. Specifically, memory CD8+ T cells recognize EBV-infected cells during latent and lytic infection. Using a symptomatic primary infection model, similar to infectious mononucleosis (IM), we found EBV induced CD8+ tissue resident memory T cells (TRMs) in mice with a humanized immune system. These human TRMs were preferentially established after intranasal EBV infection in nasal-associated lymphoid tissues (NALT), equivalent to tonsils, the primary site of EBV infection in humans. They expressed canonical TRM markers, including CD69, CD103 and BLIMP-1, as well as Granzyme B, CD107a and CCL5, while demonstrating reduced CD27 expression and proliferation by Ki-67 expression. Despite cytotoxic activity and cytokine production ex vivo, these TRMs failed to control EBV viral loads in the NALT during infection although effector memory T cells (TEMs) controlled viral titers in spleen and blood. Overall, TRMs in mucosal lymphoid tissues are established by EBV infection, but primarily systemic CD8+ T cell expansion seems to attenuate viral loads in the context of IM-like infection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/565960v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1cc2a9borg.highwire.dtl.DTLVardef@1013ea1org.highwire.dtl.DTLVardef@b6be98org.highwire.dtl.DTLVardef@19af7c7_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Human effector CD8+ T cells with an exhausted-like phenotype control tumor growth in vivo

BackgroundHumanized tumor models could be particularly valuable for cancer immunotherapy research, as they may better reflect human-specific aspects of the interfaces between tumor and immune system of human cancer. However, endogenous antitumor immunity in humanized models is still largely undefined. MethodsWe established a novel autologous humanized mouse tumor model by using NSG mice reconstituted with human immune cells from hematopoietic progenitors and tumors generated from transformed autologous human B cells. We demonstrate growth of solid lymphoid tumors after subcutaneous implantation, infiltration by endogenous human immune cells and immunocompetence of the model. FindingsWe found human T cell subsets described in human cancer, including progenitor exhausted (Tpex), terminally exhausted (Tex-term) and tissue-resident (TRM) cells in tumor-bearing humanized mice with accumulation of Tex-term and TRM in the tumor. In addition, we identified tumor-reactive CD8+ T cells through expression of CD137. This subpopulation of de novo arising human CD137+ CD8+ T cells displayed a highly proliferative, fully activated effector and exhausted-like phenotype with enhanced expression of activation and exhaustion markers like PD-1, CD39, CD160, TIM-3, TIGIT and TOX, the senescence marker CD57 (B3GAT1) and cytolytic effector molecules such as PRF1, GZMH and NKG7. Moreover, these CD137+ CD8+ T cells exhibited tumor-specific clonal expansion and presented signature overlap with tumor-reactive CD8+ T cells described in human cancer. We demonstrate superior anticancer activity of this exhausted-like human CD8+ T cell subset by adoptive transfer experiments using recipients bearing autologous human tumors. Mice adoptively transferred with CD137+ CD8+ T cells showed reduced tumor growth and higher CD8+ T cell tumor infiltration, correlating with control of human tumors. InterpretationWe established an immunocompetent humanized tumor model, providing a tool for immunotherapy research and defined effective anticancer activity of human effector CD8+ T cells with an exhausted-like phenotype, supporting clinical exploration of such cells in adoptive T cell therapies. FundingSwiss Cancer Research foundation. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSAntitumor immune responses and outcome of immunotherapeutic interventions are not always consistent between mouse models of cancer and data available in humans. This may be due to species-specific differences, therefore models with a potential for better translatability are needed, such as humanized mouse models. However, there is limited data on human antitumor T cell immunity in humanized mice. Added value of this studyIn this study, we established an immunocompetent humanized tumor model that recapitulates hallmarks of human antitumor T cell responses, offering the possibility for further translational investigation of the interface between human tumors and endogenous anticancer immunity. Furthermore, using functional in vitro assays and adoptive transfer, our study demonstrates the key importance of human effector CD8+ T cells with an activated and exhausted-like phenotype in the antitumor immune response. Implications of all the available evidenceThe autologous humanized tumor model provided in this study can serve as a tool to elucidate human-specific immune features. By bridging a gap between syngeneic mouse tumor models and human-specific antitumor immune responses, the model may help open up avenues for greater translatability of preclinical data. Our findings suggest that exhausted-like effector CD8+ T cells can be harnessed for clinical development of adoptive T cell therapies.

immunology↗

bioRxiv2023

Stem cell memory EBV-specific T cells control post-transplant lymphoproliferative disease and persist in vivo

Adoptive T cell therapy (ACT), the therapeutic transfer of defined T cell immunity to patients, offers great potential in the fight against different human diseases including difficult-to-treat viral infections but response rates are still suboptimal. Very early differentiated stem cell memory T cells (TSCM) have superior self-renewal, engraftment, persistence, and anti-cancer efficacy, but their potential for anti-viral ACT remains unknown. Here, we developed a clinically-scalable protocol for expanding Epstein-Barr virus (EBV)-specific TSCM-enriched T cells with high proportions of CD4+ T cells and broad EBV antigen coverage. These cells showed tumor control in a xenograft model of post-transplant lymphoproliferative disorder (PTLD) and were superior to previous ACT protocols in terms of tumor infiltration, in vivo proliferation, persistence, proportion of functional CD4+ T cells, and diversity of EBV antigen specificity. Thus, our new protocol may pave the way for the next generation of potent unmodified antigen-specific cell therapies for EBV-associated diseases, including tumors, and other indications.

immunology↗

bioRxiv2021

Divergent epigenetic profiles from two differentially impacted wild populationsof estuarine cordgrass (Sporobolus alterniflorus)

The effects of urbanization on watershed ecosystems present critical challenges to modern survival. Organisms in urbanized areas experience high rates of evolutionary change, but genetic adaptation alone cannot mitigate the rapid and severe effects of urbanization on biodiversity. Highly resilient, foundation species are key to maintaining an ecosystems integrity in the face of urban stressors. However, the rapid collapse and disappearance of watershed ecosystems calls into question the extent to which we can rely on such species for their services. Our research investigates the molecular mechanisms by which the foundation ecosystems provider, Sporobolus alterniflorus, adapts to life in an urbanized environment. To elucidate these mechanisms, we quantified changes in global DNA methylation (% 5-mC) as a result of acute heat stress. Specimens from two differentially impacted populations across an urban to suburban geographical transect formed the basis of this study. These two populations of Sporobolus alterniflora exhibit inverse global DNA methylation patterns when exposed to the same acute heat stress. Our findings suggest that epigenetic mechanisms, such as DNA methylation, control rapid and transient adaptation, in the form of differential stress responses, to distinct environment challenges. Highlights for manuscript submissionO_LI{blacksquare} estuarine grasses native to the Bronx River, NY face stresses associated with low dissolved oxygen and urbanization C_LIO_LI{blacksquare} differentially impacted populations of estuarine grasses exhibit inverse global DNA methylation profiles in response to acute heat stress C_LIO_LI{blacksquare} DNA methylation may represent a mechanism by which plants transiently respond to environmental stressors, and this may represent a form of rapid adaptive evolution C_LIO_LI{blacksquare} stress priming by transgenerational epigenetic modification may enhance fitness in grasses native to the heavily impacted Bronx River estuary C_LI

plant biology↗