The Genetic Drivers of Juvenile, Young, and Early-Onset Parkinson's Disease in India

BACKGROUND

Recent studies have advanced our understanding of the genetic drivers of Parkinson's disease (PD). Rare variants in more than 20 genes are considered causal for PD, and the latest PD genome-wide association study (GWAS) identified 90 independent risk loci. However, there remains a gap in our understanding of PD genetics outside of the European populations in which the vast majority of these studies were focused.

OBJECTIVE

The aim was to identify genetic risk factors for PD in a South Asian population.

METHODS

A total of 674 PD subjects predominantly with age of onset (AoO) ≤50 years (encompassing juvenile, young, or early-onset PD) were recruited from 10 specialty movement disorder centers across India over a 2-year period; 1376 control subjects were selected from the reference population GenomeAsia, Phase 2. We performed various case-only and case-control genetic analyses for PD diagnosis and AoO.

RESULTS

A genome-wide significant signal for PD diagnosis was identified in the SNCA region, strongly colocalizing with SNCA region signal from European PD GWAS. PD cases with pathogenic mutations in PD genes exhibited, on average, lower PD polygenic risk scores than PD cases lacking any PD gene mutations. Gene burden studies of rare, predicted deleterious variants identified BSN, encoding the presynaptic protein Bassoon that has been previously associated with neurodegenerative disease.

CONCLUSIONS

This study constitutes the largest genetic investigation of PD in a South Asian population to date. Future work should seek to expand sample numbers in this population to enable improved statistical power to detect PD genes in this understudied group. © 2023 Denali Therapeutics and The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Genome-Wide Polygenic Score Predicts Large Number of High Risk Individuals in Monogenic Undiagnosed Young Onset Parkinson's Disease Patients from India

Parkinson's disease (PD) is a genetically heterogeneous neurodegenerative disease with poorly defined environmental influences. Genomic studies of PD patients have identified disease-relevant monogenic genes, rare variants of significance, and polygenic risk-associated variants. In this study, whole genome sequencing data from 90 young onset Parkinson's disease (YOPD) individuals are analyzed for both monogenic and polygenic risk. The genetic variant analysis identifies pathogenic/likely pathogenic variants in eight of the 90 individuals (8.8%). It includes large homozygous coding exon deletions in PRKN and SNV/InDels in VPS13C, PLA2G6, PINK1, SYNJ1, and GCH1. Eleven rare heterozygous GBA coding variants are also identified in 13 (14.4%) individuals. In 34 (56.6%) individuals, one or more variants of uncertain significance (VUS) in PD/PD-relevant genes are observed. Though YOPD patients with a prioritized pathogenic variant show a low polygenic risk score (PRS), patients with prioritized VUS or no significant rare variants show an increased PRS odds ratio for PD. This study suggests that both significant rare variants and polygenic risk from common variants together may contribute to the genesis of PD. Further validation using a larger cohort of patients will confirm the interplay between monogenic and polygenic variants and their use in routine genetic PD diagnosis and risk assessment.

Birth Preparedness and Complication Readiness (BPACR) among brick kiln workers in Indore, India

Background

Birth preparedness and complication readiness (BPACR), promotes utilization of skilled maternal and neonatal care. Preparing for childbirth reduces delays in seeking care. Brick-kiln workers constitute a vulnerable social group who contribute to city infrastructure by laboring at low wages. 37% of the sample were Scheduled Castes, 49% Scheduled Tribes.

Methods

139 mothers of children < 2 years, residing temporarily in brick kilns of Indore were asked about preparedness for birth of youngest child. Birth preparedness was assessed by enquiring about saving money, arranging transport, identifying health facility for delivery, identified family member to accompany for labor/emergency.

Findings

10% did >3 BPACR practices implying good level of preparedness; 50% did 1-2 BPACR practices; 40% did no birth preparedness. Access to maternity benefit scheme was twice as likely to result in reasonable birth preparedness as compared to no access. Those with primary to class XII were twice as likely to practice birth preparedness as compared to those with no formal education. >3 ANC was associated with 8 percentage points greater practice of reasonable BPACR as compared to < 2 or no ANC. Mothers with knowledge of one danger sign each of pregnancy and delivery were 3 times more likely to practice BPACR than those without this knowledge. FGDs revealed challenges in access to bank account, obtaining required documents to apply for and access state maternity benefit. Lack of family support led to low BPCAR and low institutional delivery.

Conclusions

Brick-kiln women face risk of low utilization of government healthcare services. The health systems should conduct outreach antenatal care sessions in brick-kilns on knowledge of key danger signs and BPACR during health education and ANC counselling can help promote BPACR and hospital delivery. Information on requisite steps to apply for maternity benefit schemes should be shared among brick-kiln workers.

Key messages

It is crucial to promote BPACR among urban vulnerable sections, through NUHM’s outreach sessions by ANMs/ASHAs in brick-kiln, construction workers and similar groups. Access to maternity benefit cash transfer scheme should be enhanced particularly among excluded temporary urban groups such as brick-kiln workers as it is a motivation to avail hospital care.

Abstract B67: Synthetic DNA multi-neoantigen vaccine drives predominately MHC class I CD8+ T cell-mediated effector immunity impacting tumor challenge

T-cell recognition of cancer neoantigens is important for effective immune checkpoint blockade therapy, and there is increasing interest in developing personalized tumor neoantigen vaccines. Previous studies utilizing RNA and synthetic long peptide neoantigen vaccines in preclinical and early-phase clinical studies have shown immune responses predominantly driven by MHC class II CD4+ T cells. Although it has been established that CD4+ T cells are able to recognize tumor neoantigens, the majority of naturally occurring tumor antigen-specific killer T cells identified in patients have been of CD8+ origin, indicating that additional immunization strategies aimed to stimulate neoantigen-specific CD8+ T cells may be useful. Here, we report the first preclinical study utilizing a synthetic DNA vaccine platform to target tumor neoantigens in mice. For this study, we identified neoepitopes by sequencing syngeneic mouse tumors, and designed optimized DNA plasmids encoding long strings of neoepitopes separated by highly efficient cleavage sites preserving epitope integrity. We tested the immunogenicity of 84 independent neoepitopes encoded into optimized DNA plasmids delivered by adaptive electroporation in mice in vivo. We observed that this approach generated robust T-cell immunity against a similar proportion of epitopes compared to other vaccine platforms (20/84, 24%). Strikingly, however, the synthetic neoantigen DNA vaccine platform generated a much larger proportion of CD8+ T-cell responses compared to the prior studies. Synthetic neoantigen DNA vaccines generated 75% CD8+ only or CD4/CD8+ T-cell responses, and 25% CD4+ only T-cell responses, showing a dramatic and important CD8+ T-cell bias. Inclusion of only high-affinity MHC class I (<500nM) epitopes selected for a larger proportion of immunogenic epitopes, and for 100% CD8+ or CD8+/CD4+ T-cell epitopes. These neoantigen vaccines were able to control tumor growth therapeutically in vivo in both lung and ovarian cancer models, and T cells expanded from immunized mice were able to kill tumor cells ex vivo. Because of the potential for rapid synthesis of vaccine constructs, the capacity to deliver a large number of neoepitopes simultaneously, and the potent CD8+ stimulatory capacity, this advanced DNA vaccine platform represents a likely important new approach for cancer immunotherapy.

Citation Format: Elizabeth K. Duperret, Alfredo Perales-Puchalt, Regina Stoltz, G.H. Hiranjith, Nitin Mandloi, James Barlow, Amitabha Chaudhuri, Niranjan Y. Sardesai, David B. Weiner. Synthetic DNA multi-neoantigen vaccine drives predominately MHC class I CD8+ T cell-mediated effector immunity impacting tumor challenge [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B67.

Abstract A112: OncoPeptTUME: A novel computational approach analyzes the tumor microenvironment to predict response to checkpoint inhibitors

Cancer immunotherapy is now an established treatment option for many cancers. Cancer immunotherapy boosts host antitumor immunity to provide long-term benefit; however, only a small fraction of the treated patients show a durable clinical response. The tumor microenvironment ecosystem, with its complex mixture of non-malignant and malignant cells, is a major contributor in regulating the response to checkpoint blockade and development of resistance. Ongoing efforts to characterize the tumor microenvironment to stratify patients for immunotherapy and find biomarkers of response often use methods that are limited by the availability of adequate tumor tissue from needle biopsy material and loss of tissue viability during sample processing that precludes the use of single-cell sequencing platforms. Therefore, genomic methods that use deconvolution to assess the relative proportion of different cell types and their phenotypes in the tumor microenvironment are desirable for clinical use. To this end, we have developed OncoPeptTUME, a novel computational approach that utilizes a proprietary minimal gene expression signature to assign immune scores for eight broad categories of immune cells present in the tumor microenvironment. To validate the approach, we used 9,640 TCGA gene expression datasets from 33 different tumors, defined their immune cell content, organized samples into clusters based on their immune cell content, and identified the molecular differences that predict survival in samples belonging to different clusters. We further performed a deeper analysis of samples enriched in infiltrating CD8+ T-cells to identify T-cell phenotype that correlated with a long-term survival benefit. A small set of genes associated with functional T-cell phenotype was used on a dataset of melanoma samples to show that higher expression of the genes discriminated responders from the nonresponders to nivolumab treatment. In conclusion, our analysis demonstrates that OncoPeptTUME is a powerful immunogenomic tool to predict patient prognosis, stratify patients who will benefit from cancer immunotherapy and identify pathways and novel biomarkers of long-term benefit from the use of cancer immunotherapy drugs.

Citation Format: Xiaoshan Shi, Malini Manoharan, Nitin Mandloi, Sushri Priyadharshini, Laxman Iyer, Rohit Gupta, Papia Chakraborty, Amitabha Chaudhuri, Ravi Gupta. OncoPeptTUME: A novel computational approach analyzes the tumor microenvironment to predict response to checkpoint inhibitors [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A112.

A Synthetic DNA, Multi-Neoantigen Vaccine Drives Predominately MHC Class I CD8+ T-cell Responses, Impacting Tumor Challenge

T-cell recognition of cancer neoantigens is important for effective immune-checkpoint blockade therapy, and an increasing interest exists in developing personalized tumor neoantigen vaccines. Previous studies utilizing RNA and long-peptide neoantigen vaccines in preclinical and early-phase clinical studies have shown immune responses predominantly driven by MHC class II CD4⁺ T cells. Here, we report on a preclinical study utilizing a DNA vaccine platform to target tumor neoantigens. We showed that optimized strings of tumor neoantigens, when delivered by potent electroporation-mediated DNA delivery, were immunogenic and generated predominantly MHC class I-restricted, CD8⁺ T-cell responses. High MHC class I affinity was associated specifically with immunogenic CD8⁺ T-cell epitopes. These DNA neoantigen vaccines induced a therapeutic antitumor response in vivo, and neoantigen-specific T cells expanded from immunized mice directly killed tumor cells ex vivo These data illustrate a unique advantage of this DNA platform to drive CD8⁺ T-cell immunity for neoantigen immunotherapy.

A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers

A large number of tumor intrinsic and extrinsic factors determine long-term survival in human cancers. In this study, we stratified 9120 tumors from 33 cancers with respect to their immune cell content and identified immunogenomic features associated with long-term survival. Our analysis demonstrates that tumors infiltrated by CD8+ T cells expressing higher levels of activation marker (PD1hi) along with TCR signaling genes and cytolytic T cell markers (IL2hi/TNF-αhi/IFN-γhi/GZMA-Bhi) extend survival, whereas survival benefit was absent for tumors infiltrated by anergic and hyperexhausted CD8+ T cells characterized by high expression of CTLA-4, TIM3, LAG3, and genes linked to PI3K signaling pathway. The computational approach of using robust and highly specific gene expression signatures to deconvolute the tumor microenvironment has important clinical applications, such as selecting patients who will benefit from checkpoint inhibitor treatment.

Validation of liquid biopsy: plasma cell-free DNA testing in clinical management of advanced non-small cell lung cancer

Plasma cell-free tumor DNA, or circulating tumor DNA (ctDNA), from liquid biopsy is a potential source of tumor genetic material, in the absence of tissue biopsy, for EGFR testing. Our validation study reiterates the clinical utility of ctDNA next generation sequencing (NGS) for EGFR mutation testing in non-small cell lung cancer (NSCLC). A total of 163 NSCLC cases were included in the validation, of which 132 patients had paired tissue biopsy and ctDNA. We chose to validate ctDNA using deep sequencing with custom designed bioinformatics methods that could detect somatic mutations at allele frequencies as low as 0.01%. Benchmarking allele specific real time PCR as one of the standard methods for tissue-based EGFR mutation testing, the ctDNA NGS test was validated on all the plasma derived cell-free DNA samples. We observed a high concordance (96.96%) between tissue biopsy and ctDNA for oncogenic driver mutations in Exon 19 and Exon 21 of the EGFR gene. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the assay were 91.1%, 100% 100%, 95.6%, and 97%, respectively. A false negative rate of 3% was observed. A subset of mutations was also verified on droplet digital PCR. Sixteen percent EGFR mutation positivity was observed in patients where only liquid biopsy was available, thus creating options for targeted therapy. This is the first and largest study from India, demonstrating successful validation of circulating cell-free DNA as a clinically useful material for molecular testing in NSCLC.

A novel splice variant in EMC1 is associated with cerebellar atrophy, visual impairment, psychomotor retardation with epilepsy

Background

Several genes have been implicated in a highly variable presentation of developmental delay with psychomotor retardation. Mutations in EMC1 gene have recently been reported. Herein, we describe a proband born of a consanguineous marriage, who presented with early infantile onset epilepsy, scaphocephaly, developmental delay, central hypotonia, muscle wasting, and severe cerebellar and brainstem atrophy.

Methods

Genetic testing in the proband was performed using custom clinical exome and targeted next‐generation sequencing. This was followed by segregation analysis of the variant in the parents by Sanger sequencing and evaluation of the splice variant by RNA sequencing.

Results

Clinical exome sequencing identified a novel homozygous intronic splice variant in the EMC1 gene (chr1:19564510C>T, c.1212 + 1G>A, NM_015047.2). Neither population databases (ExAC and 1000 genomes) nor our internal database (n = 1,500) had reported this rare variant, predicted to affect the splicing. RNA sequencing data from the proband confirmed aberrant splicing with intron 11 retention, thereby introducing a stop codon in the resultant mRNA. This nonsense mutation is predicted to result in the premature termination of protein synthesis leading to loss of function of the EMC1 protein.

Conclusion

We report, for the first time the role of aberrant EMC1RNA splicing as a potential cause of disease pathogenesis. The severe epilepsy observed in our study expands the disease‐associated phenotype and also emphasizes the need for comprehensive screening of intronic splice mutations.

Abstract 413: Neo-epitope detection and immune infiltrate analysis of colorectal cancer samples

Colorectal cancer (CRC) is the third most common type of cancer in the United States. Targeted therapies that use monoclonal antibodies (mAbs) to EGFR have been shown to benefit some CRC patients. Until recently, KRAS has been the only predictive biomarker for anti-EGFR therapy for metastatic CRC. However, 40% to 60% of patients with wild-type KRAS do not respond to anti-EGFR therapy. Previously we have stratified 55 CRC samples by applying a RAS gene signature score which measures MEK pathway functional output independent of tumor genotype. We showed that samples that have RAS activating mutations such as KRAS and BRAF have significant higher RAS scores (p<0.001). Here, we further investigate the potential immune reactivity in these CRC samples, and thereby the potential benefit of immunotherapy, by evaluating the tumor neo-epitope burden, and the quality of immune cell infiltration based on exome-seq and RNA-seq analysis. In the 53 samples that were sequenced, 779 unique non-synonymous mutations were detected by exome-seq. These 779 mutations spanned across 263 genes. The majority of these mutations are not shared between samples (~ 5% of the mutations were shared by more than 2 samples). Several driver gene mutations were identified in this study, including KRAS, TP53, PIK3CA, APC and HER2. HLA prediction based on Exome-Seq and RNA-Seq data shows that ~86.7% of the alleles predicted to be present in 53 samples were concordant between the two RNA-seq datasets. The predicted alleles based on exome-seq and RNA-seq results have 67-69% concordance. Prediction of neo-epitopes show that HLA-binding neo-epitopes are more frequent than TCR-binding ones, and that most neo-epitopes are private and not shared between samples. A more in-depth analysis of the tumor microenvironment was performed using the RNA-seq data. The epithelial, stromal and immune content of the tumors was comparable to tumors from TCGA CRC data. Next, the immune cell compartment was further stratified into 7 different immune cell types using signatures specific to CD8 andCD4 T, T-regulatory, NK, B-cells, Macrophages and Myeloid derived suppressor cells (MDSC). The immune make up of colorectal cancer is dominated by macrophages and MDSCs. Interestingly, both granulocytic G- and monocytic M-MDSCs are present together, supporting the idea that MDSCs confer an immune suppressive microenvironment in this cancer. Significantly, high MDSC infiltrated tumors showed upregulated expression of pro-tumorigenic insulin-like growth factor pathway genes. Additionally, tumors with lower burden of MDSC showed signature of complement activation suggesting innate cell-mediated anti-tumorigenic mechanisms of tumor control in CRC. These analyses provide potential biomarkers to stratify CRC patients based on their immune reactivity and predict response to cancer immunotherapy drugs.

Citation Format: Fang Yin Lo, Nitin Mandloi, Timothy Yeatman, Kiran Paul, Ashwini Patil, Steven Anderson, Ravi Gupta, Anup Madan. Neo-epitope detection and immune infiltrate analysis of colorectal cancer samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 413. doi:10.1158/1538-7445.AM2017-413

Abstract A121: Analysis of tumor microenvironment identifies pathways predicting response to checkpoint control inhibitors: A case study comparing the immune microenvironment of uveal melanoma vs skin cutaneous melanoma

The remarkable success of checkpoint control inhibitors in treating a variety of different cancers has necessitated a deeper assessment of the tumor and its microenvironment at the genetic and phenotypic level. Data from recent clinical trials have unequivocally established that the tumor microenvironment significantly impacts the efficacy of immune-oncology drugs.

We have taken a gene expression signature-based approach to qualitatively and quantitatively assess the epithelial, stromal and immune content of tumors from RNA-seq data. The immune cell content of the tumors was further stratified to determine the infiltration pattern of nine different immune cell types including CD8+/CD4+ T-cells, Treg cells, NK cells, dendritic cells, B-cells, myeloid-derived suppressor cells (MDSC) and M1/M2 macrophages in the tumors using gene signatures specific to each immune cell type.

We applied these signatures singly, or in combination on the TCGA RNA-seq data from 33 cancers. Our analysis supports that there is an underlying molecular symmetry in tumors with higher CD8+ T-cell infiltration across most cancers characterized by the upregulation of a common set of genes that mapped to interferon signaling, antigen presentation and a pro-inflammatory cytokine network pathways. The upregulated genes were strongly correlated with patient survival in skin cutaneous melanoma (SKCM) and other cancers providing a framework for identifying biomarkers of patient response to checkpoint control inhibitors.

We present a case study to support the idea that gene expression signatures can address a critical unmet need in the immuno-oncology space, which is to create a framework for treating tumors that carry less mutation burden combined with poor T-cell infiltration. As an example, we analyzed 476 skin cutaneous melanoma (SKCM) and 80 uveal melanoma (UVM) samples from TCGA. The UVM melanoma has ∼10-fold lower median mutational burden compared to SKCM, which correlates with a lower (<10-fold) T-cell neo-epitope content in these tumors. As expected, immune cell infiltration of UVM was significantly lower compared to SKCM and so were the infiltration of different immune cell types, indicating that UVMs are immunologically barren compared to SKCMs. However, we observed interesting differences in the immune cell content of the two tumors. Whereas CD8+ T-cell infiltrated tumors were far fewer in UVM <5% compared to SKCM (∼30%), the immune microenvironment was qualitatively different in these tumors. In UVM CD8 T-cell infiltration was correlated positively with pro-inflammatory antigen presenting M1 macrophages and dendritic cells as well as immune-suppressive MDSCs, Treg cells and M2 macrophages. By contrast, CD8+ T-cell infiltrated SKCM tumors had significantly lower levels of MDSCs and M2 macrophages and were enriched in dendritic cells, M1 macrophages and Treg cells. Significantly, in UVM, the macrophage content was dominated by M2 macrophages (M1:M2, 1:2), whereas in SKCM they were similar. Taken together, our analysis suggests that in UVM, the immunesuppressive tumor microenvironment is contributed by the combined presence of MDSCs and M2 macrophages, whereas in SKCM it is contributed by the infiltration of Treg cells.

Based on our findings, we propose that therapies targeting MDSC cells, or those that can shift the balance towards increased M1 macrophage content over M2 are likely to show efficacy in UVM melanoma, which are largely unresponsive to checkpoint inhibitor molecules.

Citation Format: Ravi Gupta, Nitin Mandloi, Ashwini Patil, Malini Manoharan, Rekha Sathian, Kiran V. Paul, Amitabha Chaudhuri. Analysis of tumor microenvironment identifies pathways predicting response to checkpoint control inhibitors: A case study comparing the immune microenvironment of uveal melanoma vs skin cutaneous melanoma [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A121.