Anthony Soltis | Massachusetts Institute of Technology (MIT) (original) (raw)
Papers by Anthony Soltis
Social Science Research Network, 2018
Highlights d Multi-omic profiling of high-fat-diet-induced hepatic insulin resistance d Integrati... more Highlights d Multi-omic profiling of high-fat-diet-induced hepatic insulin resistance d Integrative modeling of omic data identifies features of hepatic insulin resistance d Obesity induces hepatocellular injury and disrupts hepatic cell-cell interactions d Enhanced hepatocyte apoptosis is a feature of obesityinduced insulin resistance
BMC Bioinformatics
Background Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel ca... more Background Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functions can be disrupted by mutation. Whole genome sequencing (WGS), on the other hand, allows for identification of non-coding somatic variation and expanded estimation of background mutation rates, yet fewer computational tools exist for specific interrogation of this space. Results We present MutEnricher, a flexible toolset for investigating somatic mutation enrichment in both coding and non-coding genomic regions from WGS data. MutEnricher contains two distinct modules for these purposes that provide customizable options for calculating sample- and feature-specific background mutation rates. Additionally, both MutEnricher modules calculate feature-level and local, or “hotspot,” somatic mutation enrichment statistics. Conclusions MutEnricher is a flexible software pac...
Respiratory Research, 2019
Background Several small molecule corrector and potentiator drugs have recently been licensed for... more Background Several small molecule corrector and potentiator drugs have recently been licensed for Cystic Fibrosis (CF) therapy. However, other aspects of the disease, especially inflammation, are less effectively treated by these drugs. We hypothesized that small molecule drugs could function either alone or as an adjuvant to licensed therapies to treat these aspects of the disease, perhaps emulating the effects of gene therapy in CF cells. The cardiac glycoside digitoxin, which has been shown to inhibit TNFα/NFκB signaling in CF lung epithelial cells, may serve as such a therapy. Methods IB3–1 CF lung epithelial cells were treated with different Vertex (VX) drugs, digitoxin, and various drug mixtures, and ELISA assays were used to assess suppression of baseline and TNFα-activated secretion of cytokines and chemokines. Transcriptional responses to these drugs were assessed by RNA-seq and compared with gene expression in AAV-[wildtype]CFTR-treated IB3–1 (S9) cells. We also compared i...
Scientific Reports
The vascular system is sensitive to radiation injury, and vascular damage is believed to play a k... more The vascular system is sensitive to radiation injury, and vascular damage is believed to play a key role in delayed tissue injury such as pulmonary fibrosis. However, the response of endothelial cells to radiation is not completely understood. We examined the response of primary human lung microvascular endothelial cells (HLMVEC) to 10 Gy (1.15 Gy/min) X-irradiation. HLMVEC underwent senescence (80–85%) with no significant necrosis or apoptosis. Targeted RT-qPCR showed increased expression of genes CDKN1A and MDM2 (10–120 min). Western blotting showed upregulation of p2/waf1, MDM2, ATM, and Akt phosphorylation (15 min–72 h). Low levels of apoptosis at 24–72 h were identified using nuclear morphology. To identify novel pathway regulation, RNA-seq was performed on mRNA using time points from 2 to 24 h post-irradiation. Gene ontology and pathway analysis revealed increased cell cycle inhibition, DNA damage response, pro- and anti- apoptosis, and pro-senescence gene expression. Based on...
Journal of Cachexia, Sarcopenia and Muscle, 2021
Spinal muscular atrophy is an inherited neurodegenerative disease caused by insufficient levels o... more Spinal muscular atrophy is an inherited neurodegenerative disease caused by insufficient levels of the survival motor neuron (SMN) protein. Recently approved treatments aimed at increasing SMN protein levels have dramatically improved patient survival and have altered the disease landscape. While restoring SMN levels slows motor neuron loss, many patients continue to have smaller muscles and do not achieve normal motor milestones. While timing of treatment is important, it remains unclear why SMN restoration is insufficient to fully restore muscle size and function. We and others have shown that SMN‐deficient muscle precursor cells fail to efficiently fuse into myotubes. However, the role of SMN in myoblast fusion is not known.
Physiological Reports, 2021
Cystic fibrosis (CF) is a life‐limiting autosomal recessive genetic disease caused by variants in... more Cystic fibrosis (CF) is a life‐limiting autosomal recessive genetic disease caused by variants in the CFTR gene, most commonly by the [F508del] variant. Although CF is a classical Mendelian disease, genetic variants in several modifier genes have been associated with variation of the clinical phenotype for pulmonary and gastrointestinal function and urogenital development. We hypothesized that whole genome sequencing of a well‐phenotyped CF populations might identify novel variants in known, or hitherto unknown, modifier genes. Whole genome sequencing was performed on the Illumina HiSeq X platform for 98 clinically diagnosed cystic fibrosis patient samples from the Adult CF Clinic at the University of California San Diego (UCSD). We compared protein‐coding, non‐silent variants genome wide between CFTR [F508del] homozygotes vs CFTR compound heterozygotes. Based on a single variant score test, we found 3 SNPs in common variants (MAF >5%) that occurred at significantly different rat...
Behavioural Brain Research, 2021
Past research has found a relationship between the apolipoprotein E (APOE) e4 allele and worse ne... more Past research has found a relationship between the apolipoprotein E (APOE) e4 allele and worse neurobehavioral functioning following mild traumatic brain injury (MTBI) in civilian populations. The purpose of this study was to examine this relationship in service members and veterans (SMVs) following MTBI. Participants were 151 SMVs (103 uncomplicated MTBI; 48 Injured Controls [IC]) prospectively enrolled in the DVBIC-TBICoE 15-Year Longitudinal TBI Study. Participants completed a battery of self-reported neurobehavioral symptom measures on average 76.2 months post-injury (SD = 31.8). APOE genotyping was undertaken using non-fasting blood samples. Participants were classified into four subgroups based on injury (MTBI vs. IC) and APOE e4 allele status (e4 present/absent). In the IC group, there were no significant differences across APOE e4 status subgroups for all measures. In the MTBI group, participants with the APOE e4 allele had significantly worse scores on measures of depressio...
Scientific Reports
Pathogenic mutations in fumarate hydratase (FH) drive hereditary leiomyomatosis and renal cell ca... more Pathogenic mutations in fumarate hydratase (FH) drive hereditary leiomyomatosis and renal cell cancer (HLRCC) and increase the risk of developing uterine leiomyomas (ULMs). An integrated proteogenomic analysis of ULMs from HLRCC (n = 16; FH-mutation confirmed) and non-syndromic (NS) patients (n = 12) identified a significantly higher protein:transcript correlation in HLRCC (R = 0.35) vs. NS ULMs (R = 0.242, MWU p = 0.0015). Co-altered proteins and transcripts (228) included antioxidant response element (ARE) target genes, such as thioredoxin reductase 1 (TXNRD1), and correlated with activation of NRF2-mediated oxidative stress response signaling in HLRCC ULMs. We confirm 185 transcripts previously described as altered between HLRCC and NS ULMs, 51 co-altered at the protein level and several elevated in HLRCC ULMs are involved in regulating cellular metabolism and glycolysis signaling. Furthermore, 367 S-(2-succino)cysteine peptides were identified in HLRCC ULMs, of which sixty were ...
Objectives: Endometrial cancer (EC) cell lines models established from diverse ancestral backgrou... more Objectives: Endometrial cancer (EC) cell lines models established from diverse ancestral backgrounds and reflective of in situ disease characteristics are necessary to support preclinical investigations with broad generalizability. We performed multi-omic analyses of EC cell line models established from women representing diverse ancestries and compared these with clinical and molecular profiling data from the TCGA UCEC patient cohort to assess the relevance of models to in situ clinical and molecular disease characteristics. Methods: Whole genome sequencing (WGS), transcriptome (RNAseq) and proteome (LC-MS/MS and RPPA) analyses were performed for primary cell line models established from endometrioid EC patients (NCI-EC1, ACI-80, ACI-181, ACI-52, ACI-61 and ACI-68) as well as commercial EC models (MFE-296, SNG-M, HEC1A, RL95-2, Ishikawa, AN3-CA, KLE). Microsatellite instability (MSI) was determined from WGS data using MSISensor2 and standard ancestry estimates by comparison with re...
Human obesity is a world-wide health crisis that promotes insulin resistance and type 2 diabetes.... more Human obesity is a world-wide health crisis that promotes insulin resistance and type 2 diabetes. Obesity increases intracellular free fatty acid concentrations in peripheral tissues, particularly the liver, which disrupts molecular mechanisms that maintain normal glycemia in response to fasting and feeding. The progression towards outright pathology in response to obesity is a highly complex process that involves coordinated dysregulation of a variety of molecular processes across multiple regulatory levels. The goal of this thesis was to apply a quantitative, multi-omic systems biology approach to the study of obesity-induce hepatic insulin resistance. We fed male C57BL/6J mice high-fat diets (HFD) to induce obesity and insulin resistance. In the first presented study, our group collected datasets to profile the hepatic epigenomes, transcriptomes, proteomes, and metabolomes of chow diet (CD) control and HFD-fed mice. I extended and applied an established computational modeling alg...
The World Journal of Biological Psychiatry
Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associat... more Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep wholegenome sequencing data in an independent population. Methods We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according to DSM-III-R diagnostic criteria. Searching only rare variants in genomic regions from recent GWAS on MDD, we used the optimized sequence kernel association test and Fischer's Exact test to fine map loci associated with severe depression. Results Our analysis identified one gene associated with severe depression, basic helix loop helix e22 (P Adjusted = 0.03) via SKAT-O test between unrelated severely depressed cases compared to unrelated non-depressed controls. The same gene BHLHE22 had a non-A c c e p t e d M a n u s c r i p t 3 silent variant rs13279074 (P Adjusted = 0.032) based on a single variant Fischer's Exact test between unrelated severely depressed cases compared to unrelated non-depressed controls. Conclusion The gene BHLHE22 shows compelling genetic evidence of directly impacting the severe depression phenotype. Together these results advance understanding of the genetic contribution to major depressive disorder in a new cohort and link a rare variant to severe forms of the disorder.
JAMA Neurology
IMPORTANCE Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by ag... more IMPORTANCE Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by age of symptom onset less than 25 years and a variable presentation. OBJECTIVE To identify the genetic variants associated with juvenile ALS. DESIGN, SETTING, AND PARTICIPANTS In this multicenter family-based genetic study, trio whole-exome sequencing was performed to identify the disease-associated gene in a case series of unrelated patients diagnosed with juvenile ALS and severe growth retardation. The patients and their family members were enrolled at academic hospitals and a government research facility between March 1, 2016, and March 13, 2020, and were observed until October 1, 2020. Whole-exome sequencing was also performed in a series of patients with juvenile ALS. A total of 66 patients with juvenile ALS and 6258 adult patients with ALS participated in the study. Patients were selected for the study based on their diagnosis, and all eligible participants were enrolled in the study. None of the participants had a family history of neurological disorders, suggesting de novo variants as the underlying genetic mechanism. MAIN OUTCOMES AND MEASURES De novo variants present only in the index case and not in unaffected family members. RESULTS Trio whole-exome sequencing was performed in 3 patients diagnosed with juvenile ALS and their parents. An additional 63 patients with juvenile ALS and 6258 adult patients with ALS were subsequently screened for variants in the SPTLC1 gene. De novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient) were identified in 3 unrelated patients diagnosed with juvenile ALS and failure to thrive. A fourth variant (p.Leu39del) was identified in a patient with juvenile ALS where parental DNA was unavailable. Variants in this gene have been previously shown to be associated with autosomal-dominant hereditary sensory autonomic neuropathy, type 1A, by disrupting an essential enzyme complex in the sphingolipid synthesis pathway. CONCLUSIONS AND RELEVANCE These data broaden the phenotype associated with SPTLC1 and suggest that patients presenting with juvenile ALS should be screened for variants in this gene.
Frontiers in Neuroscience
Traumatic brain injury (TBI) results in complex pathological reactions, where the initial lesion ... more Traumatic brain injury (TBI) results in complex pathological reactions, where the initial lesion is followed by secondary inflammation and edema. Our laboratory and others have reported that angiotensin receptor blockers (ARBs) have efficacy in improving recovery from traumatic brain injury in mice. Treatment of mice with a subhypotensive dose of the ARB candesartan results in improved functional recovery, and reduced pathology (lesion volume, inflammation and gliosis). In order to gain a better understanding of the molecular mechanisms through which candesartan improves recovery after controlled cortical impact injury (CCI), we performed transcriptomic profiling on brain regions after injury and drug treatment. We examined RNA expression in the ipsilateral hippocampus, thalamus and hypothalamus at 3 or 29 days post injury (dpi) treated with either candesartan (0.1 mg/kg) or vehicle. RNA was isolated and analyzed by bulk mRNA-seq. Gene expression in injured and/or candesartan treate...
Deep proteogenomic analyses of diverse populations will improve our understanding of molecular dr... more Deep proteogenomic analyses of diverse populations will improve our understanding of molecular drivers of disease, such as those underlying uterine neoplasms which exhibit marked racial disparities. The characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step towards investigating relationships linking patient ancestry with the proteome, genome and disease pathogenesis. We selected 1,037 nonsynonymous single nucleotide polymorphisms (nsSNPs) encoding missense amino acid substitutions occurring within putative tryptic peptides exhibiting high allele frequencies (≥ 50%) in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs) and investigated these in cell line models and tissues of uterine neoplasms collected from women representing diverse ancestries. We quantified 62 pAIMs in total across >100 patient-derived samples by multiplexed, quantitative proteomic analyses. Our ana...
Genetic mutations associated with acute myeloid leukemia can also be detected in age-related clon... more Genetic mutations associated with acute myeloid leukemia can also be detected in age-related clonal hematopoiesis, making confident assignment of detected variants to malignancy challenging particularly in the post-treatment setting. This has implications for measurable residual disease monitoring, where the relationship between sequencing and flow cytometry is also imperfect. We show, using whole-genome-sequencing informed patient-personalized single-cell DNA and antibody-oligonucleotide sequencing, that it is possible to resolve immunophenotypic identity of clonal architecture.
Social Science Research Network, 2018
Highlights d Multi-omic profiling of high-fat-diet-induced hepatic insulin resistance d Integrati... more Highlights d Multi-omic profiling of high-fat-diet-induced hepatic insulin resistance d Integrative modeling of omic data identifies features of hepatic insulin resistance d Obesity induces hepatocellular injury and disrupts hepatic cell-cell interactions d Enhanced hepatocyte apoptosis is a feature of obesityinduced insulin resistance
BMC Bioinformatics
Background Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel ca... more Background Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functions can be disrupted by mutation. Whole genome sequencing (WGS), on the other hand, allows for identification of non-coding somatic variation and expanded estimation of background mutation rates, yet fewer computational tools exist for specific interrogation of this space. Results We present MutEnricher, a flexible toolset for investigating somatic mutation enrichment in both coding and non-coding genomic regions from WGS data. MutEnricher contains two distinct modules for these purposes that provide customizable options for calculating sample- and feature-specific background mutation rates. Additionally, both MutEnricher modules calculate feature-level and local, or “hotspot,” somatic mutation enrichment statistics. Conclusions MutEnricher is a flexible software pac...
Respiratory Research, 2019
Background Several small molecule corrector and potentiator drugs have recently been licensed for... more Background Several small molecule corrector and potentiator drugs have recently been licensed for Cystic Fibrosis (CF) therapy. However, other aspects of the disease, especially inflammation, are less effectively treated by these drugs. We hypothesized that small molecule drugs could function either alone or as an adjuvant to licensed therapies to treat these aspects of the disease, perhaps emulating the effects of gene therapy in CF cells. The cardiac glycoside digitoxin, which has been shown to inhibit TNFα/NFκB signaling in CF lung epithelial cells, may serve as such a therapy. Methods IB3–1 CF lung epithelial cells were treated with different Vertex (VX) drugs, digitoxin, and various drug mixtures, and ELISA assays were used to assess suppression of baseline and TNFα-activated secretion of cytokines and chemokines. Transcriptional responses to these drugs were assessed by RNA-seq and compared with gene expression in AAV-[wildtype]CFTR-treated IB3–1 (S9) cells. We also compared i...
Scientific Reports
The vascular system is sensitive to radiation injury, and vascular damage is believed to play a k... more The vascular system is sensitive to radiation injury, and vascular damage is believed to play a key role in delayed tissue injury such as pulmonary fibrosis. However, the response of endothelial cells to radiation is not completely understood. We examined the response of primary human lung microvascular endothelial cells (HLMVEC) to 10 Gy (1.15 Gy/min) X-irradiation. HLMVEC underwent senescence (80–85%) with no significant necrosis or apoptosis. Targeted RT-qPCR showed increased expression of genes CDKN1A and MDM2 (10–120 min). Western blotting showed upregulation of p2/waf1, MDM2, ATM, and Akt phosphorylation (15 min–72 h). Low levels of apoptosis at 24–72 h were identified using nuclear morphology. To identify novel pathway regulation, RNA-seq was performed on mRNA using time points from 2 to 24 h post-irradiation. Gene ontology and pathway analysis revealed increased cell cycle inhibition, DNA damage response, pro- and anti- apoptosis, and pro-senescence gene expression. Based on...
Journal of Cachexia, Sarcopenia and Muscle, 2021
Spinal muscular atrophy is an inherited neurodegenerative disease caused by insufficient levels o... more Spinal muscular atrophy is an inherited neurodegenerative disease caused by insufficient levels of the survival motor neuron (SMN) protein. Recently approved treatments aimed at increasing SMN protein levels have dramatically improved patient survival and have altered the disease landscape. While restoring SMN levels slows motor neuron loss, many patients continue to have smaller muscles and do not achieve normal motor milestones. While timing of treatment is important, it remains unclear why SMN restoration is insufficient to fully restore muscle size and function. We and others have shown that SMN‐deficient muscle precursor cells fail to efficiently fuse into myotubes. However, the role of SMN in myoblast fusion is not known.
Physiological Reports, 2021
Cystic fibrosis (CF) is a life‐limiting autosomal recessive genetic disease caused by variants in... more Cystic fibrosis (CF) is a life‐limiting autosomal recessive genetic disease caused by variants in the CFTR gene, most commonly by the [F508del] variant. Although CF is a classical Mendelian disease, genetic variants in several modifier genes have been associated with variation of the clinical phenotype for pulmonary and gastrointestinal function and urogenital development. We hypothesized that whole genome sequencing of a well‐phenotyped CF populations might identify novel variants in known, or hitherto unknown, modifier genes. Whole genome sequencing was performed on the Illumina HiSeq X platform for 98 clinically diagnosed cystic fibrosis patient samples from the Adult CF Clinic at the University of California San Diego (UCSD). We compared protein‐coding, non‐silent variants genome wide between CFTR [F508del] homozygotes vs CFTR compound heterozygotes. Based on a single variant score test, we found 3 SNPs in common variants (MAF >5%) that occurred at significantly different rat...
Behavioural Brain Research, 2021
Past research has found a relationship between the apolipoprotein E (APOE) e4 allele and worse ne... more Past research has found a relationship between the apolipoprotein E (APOE) e4 allele and worse neurobehavioral functioning following mild traumatic brain injury (MTBI) in civilian populations. The purpose of this study was to examine this relationship in service members and veterans (SMVs) following MTBI. Participants were 151 SMVs (103 uncomplicated MTBI; 48 Injured Controls [IC]) prospectively enrolled in the DVBIC-TBICoE 15-Year Longitudinal TBI Study. Participants completed a battery of self-reported neurobehavioral symptom measures on average 76.2 months post-injury (SD = 31.8). APOE genotyping was undertaken using non-fasting blood samples. Participants were classified into four subgroups based on injury (MTBI vs. IC) and APOE e4 allele status (e4 present/absent). In the IC group, there were no significant differences across APOE e4 status subgroups for all measures. In the MTBI group, participants with the APOE e4 allele had significantly worse scores on measures of depressio...
Scientific Reports
Pathogenic mutations in fumarate hydratase (FH) drive hereditary leiomyomatosis and renal cell ca... more Pathogenic mutations in fumarate hydratase (FH) drive hereditary leiomyomatosis and renal cell cancer (HLRCC) and increase the risk of developing uterine leiomyomas (ULMs). An integrated proteogenomic analysis of ULMs from HLRCC (n = 16; FH-mutation confirmed) and non-syndromic (NS) patients (n = 12) identified a significantly higher protein:transcript correlation in HLRCC (R = 0.35) vs. NS ULMs (R = 0.242, MWU p = 0.0015). Co-altered proteins and transcripts (228) included antioxidant response element (ARE) target genes, such as thioredoxin reductase 1 (TXNRD1), and correlated with activation of NRF2-mediated oxidative stress response signaling in HLRCC ULMs. We confirm 185 transcripts previously described as altered between HLRCC and NS ULMs, 51 co-altered at the protein level and several elevated in HLRCC ULMs are involved in regulating cellular metabolism and glycolysis signaling. Furthermore, 367 S-(2-succino)cysteine peptides were identified in HLRCC ULMs, of which sixty were ...
Objectives: Endometrial cancer (EC) cell lines models established from diverse ancestral backgrou... more Objectives: Endometrial cancer (EC) cell lines models established from diverse ancestral backgrounds and reflective of in situ disease characteristics are necessary to support preclinical investigations with broad generalizability. We performed multi-omic analyses of EC cell line models established from women representing diverse ancestries and compared these with clinical and molecular profiling data from the TCGA UCEC patient cohort to assess the relevance of models to in situ clinical and molecular disease characteristics. Methods: Whole genome sequencing (WGS), transcriptome (RNAseq) and proteome (LC-MS/MS and RPPA) analyses were performed for primary cell line models established from endometrioid EC patients (NCI-EC1, ACI-80, ACI-181, ACI-52, ACI-61 and ACI-68) as well as commercial EC models (MFE-296, SNG-M, HEC1A, RL95-2, Ishikawa, AN3-CA, KLE). Microsatellite instability (MSI) was determined from WGS data using MSISensor2 and standard ancestry estimates by comparison with re...
Human obesity is a world-wide health crisis that promotes insulin resistance and type 2 diabetes.... more Human obesity is a world-wide health crisis that promotes insulin resistance and type 2 diabetes. Obesity increases intracellular free fatty acid concentrations in peripheral tissues, particularly the liver, which disrupts molecular mechanisms that maintain normal glycemia in response to fasting and feeding. The progression towards outright pathology in response to obesity is a highly complex process that involves coordinated dysregulation of a variety of molecular processes across multiple regulatory levels. The goal of this thesis was to apply a quantitative, multi-omic systems biology approach to the study of obesity-induce hepatic insulin resistance. We fed male C57BL/6J mice high-fat diets (HFD) to induce obesity and insulin resistance. In the first presented study, our group collected datasets to profile the hepatic epigenomes, transcriptomes, proteomes, and metabolomes of chow diet (CD) control and HFD-fed mice. I extended and applied an established computational modeling alg...
The World Journal of Biological Psychiatry
Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associat... more Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep wholegenome sequencing data in an independent population. Methods We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according to DSM-III-R diagnostic criteria. Searching only rare variants in genomic regions from recent GWAS on MDD, we used the optimized sequence kernel association test and Fischer's Exact test to fine map loci associated with severe depression. Results Our analysis identified one gene associated with severe depression, basic helix loop helix e22 (P Adjusted = 0.03) via SKAT-O test between unrelated severely depressed cases compared to unrelated non-depressed controls. The same gene BHLHE22 had a non-A c c e p t e d M a n u s c r i p t 3 silent variant rs13279074 (P Adjusted = 0.032) based on a single variant Fischer's Exact test between unrelated severely depressed cases compared to unrelated non-depressed controls. Conclusion The gene BHLHE22 shows compelling genetic evidence of directly impacting the severe depression phenotype. Together these results advance understanding of the genetic contribution to major depressive disorder in a new cohort and link a rare variant to severe forms of the disorder.
JAMA Neurology
IMPORTANCE Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by ag... more IMPORTANCE Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by age of symptom onset less than 25 years and a variable presentation. OBJECTIVE To identify the genetic variants associated with juvenile ALS. DESIGN, SETTING, AND PARTICIPANTS In this multicenter family-based genetic study, trio whole-exome sequencing was performed to identify the disease-associated gene in a case series of unrelated patients diagnosed with juvenile ALS and severe growth retardation. The patients and their family members were enrolled at academic hospitals and a government research facility between March 1, 2016, and March 13, 2020, and were observed until October 1, 2020. Whole-exome sequencing was also performed in a series of patients with juvenile ALS. A total of 66 patients with juvenile ALS and 6258 adult patients with ALS participated in the study. Patients were selected for the study based on their diagnosis, and all eligible participants were enrolled in the study. None of the participants had a family history of neurological disorders, suggesting de novo variants as the underlying genetic mechanism. MAIN OUTCOMES AND MEASURES De novo variants present only in the index case and not in unaffected family members. RESULTS Trio whole-exome sequencing was performed in 3 patients diagnosed with juvenile ALS and their parents. An additional 63 patients with juvenile ALS and 6258 adult patients with ALS were subsequently screened for variants in the SPTLC1 gene. De novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient) were identified in 3 unrelated patients diagnosed with juvenile ALS and failure to thrive. A fourth variant (p.Leu39del) was identified in a patient with juvenile ALS where parental DNA was unavailable. Variants in this gene have been previously shown to be associated with autosomal-dominant hereditary sensory autonomic neuropathy, type 1A, by disrupting an essential enzyme complex in the sphingolipid synthesis pathway. CONCLUSIONS AND RELEVANCE These data broaden the phenotype associated with SPTLC1 and suggest that patients presenting with juvenile ALS should be screened for variants in this gene.
Frontiers in Neuroscience
Traumatic brain injury (TBI) results in complex pathological reactions, where the initial lesion ... more Traumatic brain injury (TBI) results in complex pathological reactions, where the initial lesion is followed by secondary inflammation and edema. Our laboratory and others have reported that angiotensin receptor blockers (ARBs) have efficacy in improving recovery from traumatic brain injury in mice. Treatment of mice with a subhypotensive dose of the ARB candesartan results in improved functional recovery, and reduced pathology (lesion volume, inflammation and gliosis). In order to gain a better understanding of the molecular mechanisms through which candesartan improves recovery after controlled cortical impact injury (CCI), we performed transcriptomic profiling on brain regions after injury and drug treatment. We examined RNA expression in the ipsilateral hippocampus, thalamus and hypothalamus at 3 or 29 days post injury (dpi) treated with either candesartan (0.1 mg/kg) or vehicle. RNA was isolated and analyzed by bulk mRNA-seq. Gene expression in injured and/or candesartan treate...
Deep proteogenomic analyses of diverse populations will improve our understanding of molecular dr... more Deep proteogenomic analyses of diverse populations will improve our understanding of molecular drivers of disease, such as those underlying uterine neoplasms which exhibit marked racial disparities. The characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step towards investigating relationships linking patient ancestry with the proteome, genome and disease pathogenesis. We selected 1,037 nonsynonymous single nucleotide polymorphisms (nsSNPs) encoding missense amino acid substitutions occurring within putative tryptic peptides exhibiting high allele frequencies (≥ 50%) in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs) and investigated these in cell line models and tissues of uterine neoplasms collected from women representing diverse ancestries. We quantified 62 pAIMs in total across >100 patient-derived samples by multiplexed, quantitative proteomic analyses. Our ana...
Genetic mutations associated with acute myeloid leukemia can also be detected in age-related clon... more Genetic mutations associated with acute myeloid leukemia can also be detected in age-related clonal hematopoiesis, making confident assignment of detected variants to malignancy challenging particularly in the post-treatment setting. This has implications for measurable residual disease monitoring, where the relationship between sequencing and flow cytometry is also imperfect. We show, using whole-genome-sequencing informed patient-personalized single-cell DNA and antibody-oligonucleotide sequencing, that it is possible to resolve immunophenotypic identity of clonal architecture.